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PROTEOGRAPH ANALYSIS SUITE USER GUIDE
ProteographTM Product Suite
FOR FIELD TESTING USE ONLY
FOR USE WITH
SP100 Automation Instrument ProteographTM Instrument Control Software ProteographTM Assay Kit
ProteographTM PQR Labware Kit
seer.bio

Notice
© 2021 Seer, Inc. All rights reserved. Information in this document is subject to change without notice. Seer assumes no responsibility for any errors or omissions in this document. Duplication and/or reproduction of all or any portion of this document without the express written consent of Seer is strictly forbidden. Seer does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.
Nothing contained herein shall constitute any warranty, express or implied, as to the performance of any products described herein, or any warranties of merchantability, fitness for a particular purpose or non-infringement. The use of products described herein is subject to certain restrictions as set forth in the applicable terms and conditions of sale or license accompanying the purchase of such product and any written agreements between Seer and user. Seer may refer to products or services offered by other companies by their brand names or company names solely for clarity and does not claim any rights in those third party marks or names. All products and services described herein are intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s).
Failure to completely read and explicitly follow all of the instructions contained herein may result in damage to the product(s), injury to persons, including to users or others, and damage to other property, and will void any warranty applicable to the product(s). Seer does not assume any liability arising out of the improper use of the product(s) described herein (including parts thereof or software).
BUYER IS NOT LICENSED OR AUTHORIZED TO, AND AGREES NOT TO, USE ANY SEER PRODUCT FOR ANY CLINICAL OR DIAGNOSTIC PURPOSES.
Notice
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 2

Revision history
DOCUMENT DATE DESCRIPTION OF CHANGE
CF-1016 A November 2021 Initial release
Revision history
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 3

Contents
Notice
Revision history Contents
Chapter 1 Proteograph Overview
Introduction
Highlights
Proteograph Assay steps SP100 Automation Instrument
Instrument computer Software packages
Work deck and autoload tray Work deck layout
Serial number Instrument hardware
Barcode reader
Carriers
Chiller unit and chiller power unit Compressed O-ring expansion head Gantry
Heater shaker
Independent 8-channel pipette heads Magnetic plate
MPE module and MPE power unit Plate grippers
Teaching needles
Waste containers
ProteographTM Instrument Control Software Methods
ProteographTM Assay Kit Refrigerated box
Room-temperature box Additional required materials Deionized water quality requirements Trap column recommendation
Chapter 2 Proteograph Assay
Proteograph Assay method
Materials for the Proteograph Assay method Number of samples and controls
Peptide Collection Plate
Best practices Pipetting
Loading labware
Placing lids
Work deck quick reference Turn on the instrument
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Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY
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Prepare materials
Set up the method Set up the work deck
Load reagents and plates
Load solutions and reservoirs
Load samples, controls, and nanoparticles Check labware
Scan barcodes and start the method
Clean the instrument
Chapter 3 Peptide Quantification
Peptide Quantification method
ProteographTM PQR Labware Kit
Additional materials for the Peptide Quantification method Turn on the instrument
Prepare the quantification consumables
Run the Peptide Quantification method
Chapter 4 Peptide Reconstitution
Peptide Reconstitution method
Additional materials for the Peptide Reconstitution method Peptide Reconstitution Buffer preparation
Equipment
Reagents and materials Preparation steps
Turn on the instrument
Prepare the files needed for the Peptide Reconstitution method
Prepare the peptide quant data file
Prepare the partial plate map file Prepare the reconstitution consumables Run the Peptide Reconstitution method
Chapter 5 Instrument Maintenance
Maintenance methods
Preventative maintenance
Materials for maintenance methods Run the Daily Maintenance method
Run the Weekly Maintenance method
Hardware cleaning requirements Run the MPE Flush method
Run the Water Run method
Chapter 6 Troubleshooting
Resolve error messages
Carrier Scan Error
Cognex Initialization Error
Misaligned labware
Lack of pressurized gas or low pressure error No Barcode Scanned
NTR Scan Error
Pause a method
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Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY
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Abort a method
Package trace files
Appendix A Automation
Proteograph Assay processes
Appendix B Safety and Compliance
Safety considerations and markings
Intended use Instrument operation
Emergency shutoff Safety hazards
Laser beam
Electromagnetic radio frequency Electrostatic charge
Regulatory compliance Product certification CSA C/US mark
CE Mark
RoHS directive FCC compliance Conformité IC
Glossary
Index
Technical Support
Contact Information
Telephone
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Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY
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Chapter 1
Proteograph Overview
This chapter introduces you to the main components of the Seer ProteographTM Product Suite.

Chapter 1 Proteograph Overview Introduction
Introduction
The Seer ProteographTM Product Suite provides an integrated workflow for unbiased, deep, and large-scale access to the proteome. Combined with proprietary engineered nanoparticles, the Seer SP100 Automation Instrument prepares peptides for analysis on most mass spectrometry (MS) platforms configured for proteomics. The ProteographTM Analysis Suite (PAS) easily integrates the analysis of raw MS data, quality control (QC) reporting, and data visualization to empower proteomics insights quickly and at scale.
Paired with MS, the Proteograph Product Suite simplifies proteome analysis, offering a rapid, integrated workflow to convert proteins into peptides for deep analysis of the proteome. The following figure shows the high-level steps in the workflow with the products used at each step.
Figure 1. Proteograph workflow
Highlights
The ProteographTM Product Suite features the following products:
• SP100 Automation Instrument
– Intuitive ProteographTM Instrument Control Software (ICS) for experiment setup and instrument
operation
– Custom Proteograph Assay method that processes proteins in a typical 8-hour workday
– Dedicated methods for instrument maintenance and troubleshooting
• ProteographTM Assay Kit
– Proprietary panel of five engineered nanoparticles for processing up to 16 samples in one 96-well
plate
– Buffers and reagents for protein lysis, digestion, and peptide purification
– Quality controls to easily compare results across assays or troubleshooting for a specific assay
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 8

Chapter 1 Proteograph Overview Proteograph Assay steps
Proteograph Assay steps
The Proteograph Assay method runs on the SP100 Automation Instrument and outputs MS-ready peptides. The following table summarizes the method steps and durations. For a detailed breakdown of each step, see Proteograph Assay processes (page 75).
Table 1. Summary of the Proteograph steps
APPROXIMATE CUMULATIVE DESCRIPTION TIME TIME (HOURS)*
Proteograph Assay method setup 30 minutes
0.5
Sample dispensing and nanoparticle transfer 29 minutes
1.0
Protein corona formation 1 hour
2.0
Protein corona wash 36 minutes
2.6
Protein corona denaturation 40 minutes
3.3
Protein digestion 3 hours and 13 minutes
6.5
Peptide cleanup, wash, and elution 49 minutes
7.3
STOPPING POINT
Deck cleanup 10 minutes
7.5
Peptide quantification 30 minutes
8.0
Peptide reconstitution 25 minutes
DRY OVERNIGHT
8.4
*Rounded up to the nearest tenth of an hour.
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Chapter 1 Proteograph Overview SP100 Automation Instrument
SP100 Automation Instrument
The SP100 Automation Instrument automates the pipetting of liquids to prepare peptides for downstream analysis. A custom table holds the instrument and stores the monitored multi-flow positive pressure evaporative extraction (MPE) power unit, chiller unit, and instrument computer. For specifications, see the SP100 Automation Instrument Site Prep Guide (CF-1017 B).
An adjustable arm affixed to the custom table presents the touchscreen monitor. The touchscreen is glove- compatible and displays the ICS user interface.
Figure 2. SP100 installed on the custom table
Instrument computer
The front panel of the instrument computer includes a power switch and two USB ports for transferring data to a portable device.
Figure 3. Instrument computer with power and auxiliary connections
A Power switch
B USB ports
A Instrument
B Touchscreen monitor
C Custom table
NOTE
The touchscreen monitor also has USB ports that are more readily accessible than those on the instrument computer.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 10

Chapter 1 Proteograph Overview SP100 Automation Instrument
Software packages
The following software packages are preinstalled on the instrument computer and appear on its desktop:
• ProteographTM Instrument Control Software (ICS)
• Seer Support Package Creator
• Microlab Star Maintenance & Verification
• Microlab STAR Verification 2
• Hamilton Method Editor
• Hamilton Run Control
• Hamilton CO-RE Liquid Editor
• DataMan Setup Tool
The Proteograph ICS package launches ICS and the Seer Support Package Creator generates files for troubleshooting (see Package trace files (page 73)). The remaining packages are used by Seer support personnel only.
Work deck and autoload tray
The SP100 has two work surfaces, the work deck and the autoload tray. Enclosed by a front protective cover, the work deck is the area inside the instrument that holds the carriers. The autoload tray is the surface in front of the instrument. It includes 30 tracks, labeled in increments of five, that guide carriers as they move in and out of the instrument.
The black bumpers on the front of the autoload tray are slide blocks that guide the carriers as they move along tracks between the work deck and the autoload tray. Stop hooks attached to the back of the autoload tray secure carriers and provide a stop point so that carriers are completely inserted.
Figure 4. Work surfaces
A Work deck B Autoload tray C Stop hooks D Side blocks
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Work deck layout
The following figure shows how the carriers and built-in components are arranged on the work deck. Table 2 indicates the placement of labware for the Proteograph Assay method.
Figure 5. Empty work deck
Table 2. Labware positions for the Proteograph Assay method
CARRIER POSITION ITEM NOTE
Tube Carrier 1 T1–T16 Sample Tubes 01–16
T17 Plasma Control
T18 MPE Control
T19–T32 Empty
Tube Carrier 2 T33–T37 Nanoparticle Tubes (NP #1–5)
T38–T64 Empty
Plate Carrier A A1 Peptide Cleanup Plate
A2 Wash C Solution Single Reservoir
A3 Cleanup Reagents 4-Well Reservoir
A4 Sample Prep Plate
A5 Intermediate Plate
1
1
1, 2
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Chapter 1 Proteograph Overview SP100 Automation Instrument
CARRIER POSITION ITEM NOTE
Reservoir Carrier R1 Control Dilution Solution Reservoir
R2 Denaturing Solution Reservoir
R3 Reduction Solution Reservoir
R4 Alkylation Solution Reservoir
R5 Deionized Water Reservoir 1
Plate Carrier B B1 Empty
B2 Intermediate Plate 1
B3 Intermediate Plate
B4 Empty
B5 Peptide Collection Plate 1
Tip Carrier C C1 Empty
C2 1 Stack of 300 μL Nested Conductive Tips (NCTs) 3
C3 1 Stack of 300 μL NCTs 3
C4 1 Stack of 300 μL NCTs 3
C5 1 Stack of 300 μL NCTs 3
Stationary in Work Deck D1 1 Stack of 300 μL NCTs 3
D2 1 Stack of 300 μL NCTs 3
1This labware is loaded empty. 2One stack of four plates. 3One stack of four NCT racks.
Serial number
A nameplate is mounted on the inside of the instrument, on the left side of the work deck behind the protective front cover. The nameplate includes the instrument serial number, model, electrical information, and certification information.
Instrument hardware
The SP100 is equipped with the following hardware, which pipettes liquids in labware and transports plates. All hardware components reside inside the instrument, except for the external waste containers and carriers, which move in and out of the instrument.
Labels affixed to the instrument hardware identify safety considerations and hazards. For a list of labels with descriptions, see Safety hazards (page 80).
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Barcode reader
Before starting a method, the barcode reader scans all barcode-labeled plates, reservoirs, and tubes to ensure proper setup.
Carriers
Guided to predetermined positions, the carriers are movable units that hold labware and move between the autoload tray and the work deck. The instrument uses three types of carriers for different labware: tubes, plates, and reservoirs. For a schematic of the carriers, see Work deck layout (page 12).
Figure 6. Tube, plate, reservoir, and tip carriers
A Tube Carriers 1 and 2
B Plate Carrier A
C Reservoir Carrier
D Plate Carrier B
E Tip Carrier C
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Chiller unit and chiller power unit
During the method, the chiller unit maintains the Trypsin/LysC 8-Well reservoir at the appropriate temperature. The chiller power unit (an instrument peripheral) controls power to the chiller unit.
Figure 7. Chiller unit Figure 8. Chiller power unit
A Power switch (not shown; located in the upper- left corner of the back panel)
Compressed O-ring expansion head
Attached to the moving gantry, the compressed O-ring expansion (CO-RE) head enables simultaneous 96-well liquid handling throughout the method. Do not touch the CO-RE head during operation.
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Gantry
During the method, the gantry moves the CO-RE head and independent 8-channel pipette heads. Do not touch the gantry during operation.
Heater shaker
The heater shaker incubates and continuously mixes the Sample Prep Plate. During the Proteograph Assay method, the heater automatically heats to the appropriate temperature and reaches 95 °C for sample denaturing.
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Independent 8-channel pipette heads
Attached to the gantry, the independent 8-channel pipette heads provide eight separate channels for liquid handling. Do not touch the heads during instrument operation.
Magnetic plate
The magnetic plate is an Alpaqua Magnum FLX, a solid-core ring magnet used to pull down nanoparticles during corona washing and peptide transfer. Integrated spring-cushion technology optimizes performance. The magnetic plate always remains inside the instrument.
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Chapter 1 Proteograph Overview SP100 Automation Instrument
MPE module and MPE power unit
The MPE module uses positive pressure to collect and purify peptides from the Peptide Cleanup Plate. During wash steps, the MPE module sends liquid waste to an external container. The MPE power unit (an instrument peripheral) controls power to the MPE module.
Figure 9. MPE module
Figure 10. MPE power unit
A MPE module
B Filter plate holder
C Filter tray
A MPE power unit
B MPE power button (which glows green when on)
Plate grippers
Channels 7 and 8 of the independent 8-channel pipette heads use the plate grippers. Do not move the plate grippers from positions 2 and 3 of the plate gripper tray.
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Chapter 1 Proteograph Overview SP100 Automation Instrument
Teaching needles
A set of eight teaching needles are used to check pressure tightness of the pipetting channels during maintenance.
Waste containers
The following containers collect waste from the SP100. Clear bags in the pipette and core waste bins direct waste to a separate biohazard container. The biohazard container is lined with a red, labeled biohazard bag.
• Independent 8-channel pipette head waste — Waste bin for the 8-channel conductive 300 μL tips
• CO-RE head waste — Waste bin for 300 μL NCTs from the CO-RE head
• MPE waste — Liquid waste container for all liquid waste, the majority being the MPE waste from wash steps (wash buffers and plasma)
CAUTION
Avoid removing the teaching needles from the work deck. Without the teaching needles, the Daily Maintenance and Weekly Maintenance methods fail.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 19

Chapter 1 Proteograph Overview SP100 Automation Instrument
ProteographTM Instrument Control Software
The instrument includes dedicated software, ICS, that controls instrument operations and provides an interface for running a method and maintaining the instrument.
Figure 11. Proteograph ICS main menu
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 20

Chapter 1 Proteograph Overview SP100 Automation Instrument
Methods
ICS includes the following methods to prepare peptides for MS, maintain the instrument, and troubleshoot.
ICON METHOD PURPOSE
Proteograph Assay Peptide preparation
Peptide Quantification Peptide preparation
Peptide Reconstitution Peptide preparation
Daily Maintenance Instrument maintenance
Weekly Maintenance Instrument maintenance
MPE Flush Instrument maintenance and troubleshooting
Water Run Training and troubleshooting
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 21

Chapter 1 Proteograph Overview ProteographTM Assay Kit
ProteographTM Assay Kit
The Proteograph Assay method requires the Seer Proteograph Assay Kit (PN S55R1100) and materials from third-party vendors. The kit ships in one box that contains a refrigerated box of reagents and room-temperature labware. When you receive the kit, promptly remove the refrigerated box and store at 2 °C to 8 °C.
For information about third-party materials, see Additional required materials (page 24). Refrigerated box
Table 3. Contents of the Seer Proteograph Assay Kit refrigerated box
DESCRIPTION QUANTITY CAP COLOR / LABEL VOLUME
Alkylation Solution 1 Green 7 mL
Control Dilution Solution 1 White 10 mL
Denaturing Solution 1 Denature 25 mL
Digestion Stop Solution 1 Red 7 mL
Elution Solution 1 Elution 20 mL
Enzyme Reconstitution Solution 1 White 7 mL
MPE Control 1 Clear with black ring 80 μL
MS Control 1 Clear with black ring 24 μL
Nanoparticle #1 (NP #1) 1 Clear with black ring 85 μL
Nanoparticle #2 (NP #2) 1 Clear with black ring 58 μL
Nanoparticle #3 (NP #3) 1 Clear with black ring 60 μL
Nanoparticle #4 (NP #4) 1 Clear with black ring 343 μL
Nanoparticle #5 (NP #5) 1 Clear with black ring 90 μL
Peptide Wash Solution A 1 Wash A 40 mL
Peptide Wash Solution B 2 Wash B 27 mL
Plasma Control 1 Clear with black ring 150 μL
Reduction Solution 1 Blue 7 mL
Trypsin/LysC Protease MS Grade 6 Gray 100 μl
Wash Solution C 2 White 100 mL
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Chapter 1 Proteograph Overview ProteographTM Assay Kit
Room-temperature box
Table 4. Contents of the Seer Proteograph Assay Kit room-temperature box
DESCRIPTION QUANTITY
Alkylation Solution Reservoir 1
Black Plate Lid 3
Cleanup Reagents 4-Well Reservoir 1
Clear Plate Lid 1
Control Dilution Solution Reservoir 1
Deionized Water Reservoir 1
Denaturing Solution Reservoir 1
Intermediate Plate 6
Peptide Cleanup Plate (with plate holder) 1
Peptide Collection Plate 1
Reduction Solution Reservoir 1
Sample Prep Plate 1
Sample Tubes 01–16 16
Trypsin/LysC 8-Well Reservoir 1
Wash C Solution Single Reservoir 1
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 23

Chapter 1 Proteograph Overview Additional required materials
Additional required materials
Peptide preparation, quantification, and reconstitution — as well as instrument maintenance — require the consumables and equipment listed in the following table. Purchase these materials from the indicated suppliers.
DESCRIPTION SUPPLIER NOTES
1–10 mL pipette with tips Rainin, material # 17011783
20–200 μL multichannel pipette with tips Rainin, material # 17013810
20–200 μL pipette with tips Rainin, material # 17014391
70% isopropyl alcohol or 70% ethanol General lab supplier
100–1000 μL pipette with tips Rainin, material # 17014382
300 μL Nested Conductive Tips Hamilton, part # 235950
Acid-Resistant CentriVap Centrifugal Vacuum Concentrator Labconco, catalog # 7810016 (speed vac)
Aluminum Sealing Foil 5 × 3 Inch VWR, catalog # 60941-126
Axygen AxyMats 96 Round Well Sealing Mat for PCR Microplates VWR, product # AM-96-PCR-RD
Deionized water General lab supplier
Disposable latex gloves General lab supplier
Eppendorf 96-Well Protein LoBind Deep Well Plates Fisher Scientific, E0030504305 1
Lab coats General lab supplier
Peptide Reconstitution Buffer Seer, contact support@seer.bio 2
PierceTM Quantitative Fluorometric Peptide Assay Thermo Fisher, catalog # 23290
Protective goggles General lab supplier
Refrigerated Microcentrifuge Thermo Scientific, catalog # 3 75002441
Waste Bags with Biohazard Labeling Hamilton, part # 199203
Waste Container Biohazard Box Hamilton, part # 281520
1Or equivalent proteomics-compatible 96-well plate.
2Or equivalent laboratory-prepared reconstitution buffer; see Peptide Reconstitution Buffer preparation (page 52). 3Or equivalent.
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Chapter 1 Proteograph Overview Deionized water quality requirements
Deionized water quality requirements
In its own testing laboratory, Seer uses a PURELAB Chorus 1 Complete water purification system to produce deionized water for the assay. Seer recommends that the water purification system you use to produce deionized water meets or exceeds the following specifications.
PRODUCT SPECIFICATIONS PURELAB CHORUS 1 COMPLETE 10L/HR NOTE
Dispense Flowrate >1.5 l/min
Inorganics (resistivity at 25 °C) 18.2 MΩ.cm
Organics (TOC) <5 ppb
Bacteria <0.001 CFU/ml *
Bacterial Endotoxin <0.001 EU/ml *
pH Effectively Neutral
Particles 0.2 μm *
DNase < 5 pg/ml
RNase < 1 pg/ml Daily Usage (max) 100 l/day Daily Usage (min) 1 l/day Delivery Flow Rate 10 l/hr *With point-of-use filter fitted. Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 25 Chapter 1 Proteograph Overview Trap column recommendation Trap column recommendation Seer recommends the use of a trap column coupled to the LC-MS system used for analysis. A trap column removes contaminants and unwanted analytes that could interfere with the analysis of analytes of interest. For assistance with selecting a suitable trap column for your organization’s use, contact support@seer.bio. Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 26 Chapter 2 Proteograph Assay This chapter provides instructions on how to prepare and load the Proteograph Assay labware and reagents on the Seer SP100 Automation Instrument. Chapter 2 Proteograph Assay Proteograph Assay method Proteograph Assay method Run the Proteograph Assay method on the SP100 Automation Instrument to prepare peptides for analysis. To run the method, prepare the instrument and materials and follow the ICS prompts to set up the work deck. After the method starts, the instrument automatically performs the steps to convert proteins into peptides. Subsequent quantification and reconstitution ensure the appropriate volume and concentration for downstream LC-MS. Before proceeding, complete the following prerequisites: • Review safety and regulatory information to ensure safe and correct instrument operation. See Safety and Compliance (page 77). • Confirm you have all Proteograph Assay Kit items and other materials. See Kit contents and storage and Additional required materials (page 24). • Review best practices to help load the work deck correctly and efficiently. See the information in Best practices (page 30). Materials for the Proteograph Assay method The Proteograph Assay method requires the following materials. (For supplier information, see Additional required materials (page 24).) • 300 μL Nested Conductive Tips (NCTs) • Deionized water • Personal protective equipment – Disposable latex gloves – Lab coats – Protective goggles • Pipettes with tips – 1–10 mL pipette with tips – 20–200 μL pipette with tips – 100–1000 μL pipette with tips • Proteograph Assay Kit • Refrigerated Microcentrifuge Number of samples and controls The Proteograph Assay method requires 16 plasma samples. Each sample incubates separately with each of the five nanoparticles, resulting in 80 wells of peptides in a 96-well plate. To ensure consistent quality and help with troubleshooting, three additional wells are dedicated to the following controls: Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 28 Chapter 2 Proteograph Assay Proteograph Assay method • Process Control — A mixture of the plasma control (itself a mixture of pooled plasma samples) and Nanoparticle #1. It is exposed to every step, including corona formation, trypsin digestion, and peptide cleanup. • Digestion Control — A mixture of the plasma control and the control dilution solution. It is added to the plate after corona formation and exposed to the trypsin digestion and peptide cleanup steps. • MPE Control — A purified mixture of commercially available pre-digested peptides. It is added to the plate after tryspin digestion and exposed to the peptide cleanup step. Peptide Collection Plate The output of the Proteograph Assay method is the Peptide Collection Plate. Samples and nanoparticles occupy all wells in columns 1–10 and controls occupy wells A11, B11, and C11. For example, Sample 1 occupies well A1 with NP #1, well A2 with NP #2, and so on. Figure 12. Layout of the final Peptide Collection Plate Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 29 Chapter 2 Proteograph Assay Best practices Best practices When setting up the work deck, apply the following best practices to ensure the proper techniques for pipetting liquids, placing labware and reagents, and placing lids. Improper work deck setup can cause errors. (For information on resolving setup errors, see Troubleshooting (page 68).) Pipetting When pipetting samples to Proteograph sample tubes, observe the following best practices to avoid the formation of bubbles. • After spinning down the tube, carefully aspirate 250 uL from it, avoiding lipid layers and residuals at the bottom of the tube. • Slowly dispense plasma at the bottom of the sample tube with the tip touching the side of the tube. • While dispensing, avoid using the second stop of the pipette so as not to introduce bubbles. • If a bubble is present after dispensing, use a dry pipette tip to pop the bubble. For small bubbles, use a small pipette tip, e.g., a p200 or p20 tip. • If a bubble will not burst, carefully aspirate just on top of the bubble to remove it. Loading labware When loading labware onto the work deck, observe the following best practices for holding tubes, placing labware, loading carriers, barcode orientation, tube placement, and labware orientation. • Tubes — Hold tubes at the top to avoid warming samples in your hand. Avoid placing your fingers over barcodes. Face all tube barcodes to the right so the barcode reader can scan them. Incorrect orientation makes the barcodes unreadable. Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 30 Chapter 2 Proteograph Assay Best practices Fully insert tubes into the tube carrier. Improper seating can cause malfunction. • Reservoirs — Fully insert reservoirs into the reservoir carrier. • Wells — Position wells on plate carriers so that well A1 is in the upper-left corner. • Plates — Fully seat plates on the plate carriers. Misaligned plates cause collision or malfunction. Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 31 Chapter 2 Proteograph Assay Best practices • Carriers — Push all carriers to the stop hooks at the back of the autoload tray. Incorrect positioning causes collision or malfunction. Do not pull carriers out during method runs. Placing lids Properly place lids on top of plates. The plate grippers cannot pick up a plate with a misaligned lid. Figure 13. Misaligned lid Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 32 Chapter 2 Proteograph Assay Work deck quick reference Work deck quick reference The following figure shows the layout of the work deck after it is loaded with labware and reagents for the Proteograph Assay method. If you are: • A new user, refer to the figure to confirm proper work deck layout before starting the method. • An experienced user, use the figure as a quick reference when loading the work deck. Figure 14. Work deck loaded for the Proteograph Assay method Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 33 Chapter 2 Proteograph Assay Turn on the instrument Turn on the instrument Turning on the SP100 ensures that the instrument and peripherals are communicating and ready to start the method. When not in use, the instrument and peripherals are turned off. 1. Turn on the following hardware: – SP100 — Press the green switch on the front of the instrument. – MPE power unit — Press the power button on the front of the MPE power unit. – Chiller power unit — Press the power switch on the back panel of the chiller power unit. – Instrument computer — Press the power button on the front of the instrument computer. 2. Check the gas supply for appropriate pressure. 3. Confirm that the MPE regulator (located near the MPE waste container) is set to > 110 psi.
4. After the computer has initialized, select the Proteograph ICS desktop shortcut to launch ICS.
5. Open the front protective cover and pull the carriers onto the autoload tray.
6. Push the carriers to the stop hooks at the back of the autoload tray.
7. Check that the carriers are secure.
8. Close the front protective cover.
9. Run the Daily Maintenance method. For instructions, see Run the Daily Maintenance method (page 63). When the Daily Maintenance method is complete, ICS returns to the main menu.
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Chapter 2 Proteograph Assay Prepare materials
Prepare materials
1. Set the centrifuge to 4 °C.
2. Verify that the chiller unit reads 4–5 °C. If it does not, verify that the chiller unit is set to that temperature
and wait until that temperature is achieved.
3. If plasma samples are frozen, remove them from -85 °C to -15 °C storage and thaw in an ice-water bath.
4. Remove labware from room-temperature storage and arrange as follows.
– Place the Black Plate Lid and Trypsin/LysC 8-Well Reservoir on ice.
– Check all labware for appropriate barcode labels.
Intermediate Plates and the Peptide Cleanup Plate do not have a barcode label.
5. Remove the refrigerated box from 2 °C to 8 °C storage and arrange reagents as follows.
– Place the Enzyme Reconstitution Solution on ice.
– Place the six tubes of Trypsin/LysC Protease MS Grade on ice.
– Set aside the remaining reagents at room temperature.
TIP
If the chiller unit is set to but is not achieving 5 °C, contact support@seer.bio
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Chapter 2 Proteograph Assay Set up the method
Set up the method
1. On the ICS main menu, select Proteograph Assay.
2. At the Sign In stage:
a. Enter your username (up to 20 alphanumeric characters, including commas, dashes, periods,
spaces, and underscores).
b. Select Continue.
3. At the Experiment Registration stage:
a. In the Experiment Name field, enter a name for your experiment.
b. In the Plate Name field, enter a unique name for the Proteograph run.
c. Select Continue.
Each name can contain up to 20 alphanumeric characters and underscores.
4. At the Device Initialization stage:
a. Confirm that the MPE power unit, chiller power unit, and instrument computer are turned on.
b. Open the front protective cover.
c. Pull the carriers onto the autoload tray.
d. Push the carriers to the stop hooks at the back of the autoload tray.
e. Check that the carriers are secure.
f. Close the front protective cover.
g. Select Continue.
5. Open the front protective cover.
6. At the Tip Counter stage, check for sufficient 300 μL NCTs:
– Confirm the Total Tips Remaining field matches the number of NCTs on the work deck.
– Confirm the Stack Height field matches the number of racks on the work deck.
7. If the ICS indicates an insufficient number of NCTs, the NCT arrangement is incorrect, or each stack
contains fewer than two full racks, refill the NCTs:
a. Replace both stacks in Positions D1 and D2 with two full stacks (four racks).
b. Select the Refill All Eight (8) NTRs checkbox.
c. Select Refill.
d. When ICS updates the NTR Details, confirm the new NCT arrangement.
TIP
If an experiment requires multiple plates, use the same experiment name for each plate to group the plates for analysis.
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Chapter 2 Proteograph Assay Set up the method
ICS updates the NTR Details.
8. Select Continue.
NOTE
The nested tip rack (NTR) holds the NCTs. Four NTRs equals one stack.
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Chapter 2 Proteograph Assay
Set up the work deck
Set up the work deck
A series of Deck Setup stages guide you through setting up the work deck.
Load reagents and plates
At the Deck Setup 1 of 3 stage:
1. Pull the following six carriers from the work deck to the autoload tray:
– Tube carriers (2)
– Plate carriers (2)
– Reservoir carrier (1)
– Tip carrier (1)
2. Place the Peptide Cleanup Plate, including the plate holder, into position A1.
3. Place the Wash C Solution Single Reservoir into position A2.
4. Add two bottles of Wash Solution C to the Wash C Solution Single Reservoir. Cover with a Black Plate Lid.
5. Load the Cleanup Reagents 4-Well Reservoir:
a. Place the reservoir into position A3.
b. Pouring reagents from the front of the reservoir, add reagents to each well as follows.
– Well 1 — Digestion Stop Solution (1 bottle)
– Well 2 — Peptide Wash Solution A (1 bottle)
– Well 3 — Peptide Wash Solution B (2 bottles)
– Well 4 — Elution Solution (1 bottle)
c. Cover the reservoir with a Black Plate Lid.
6. Place the Sample Prep Plate into position A4. Cover with a Clear Plate Lid.
CAUTION
For all pipetting steps, make sure all liquid is in the bottom of the tube. Do not leave droplets on the sides of the tube or in caps.
TIP
Pouring reagents from the front of the reservoir prevents cross-contamination between wells.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 38

Chapter 2 Proteograph Assay
Set up the work deck
7. Load the Intermediate Plates:
a. Stack four plates in position A5. b. Place one plate into position B2. c. Place one plate into position B3.
8. Place one Peptide Collection Plate into position B5.
9. Place a stack of NCTs into each of positions C2–C5.
10. Verify that there are enough tips in positions D1 and D2.
11. Perform the following steps on ice:
a. Add 500 μL Enzyme Reconstitution Solution to one tube of Trypsin/LysC Protease MS Grade for a final concentration of 0.2 ug/μL.
b. Pipette 2–3 times to mix.
c. Repeat steps a and b for the remaining five Trypsin/LysC tubes.
d. Transfer 500 μL from each Trypsin/LysC tube into row A of the Trypsin/LysC 8-Well Reservoir.
e. Cover the reservoir with a Black Plate Lid.
12. Place the Trypsin/LysC 8-Well Reservoir into the 5 °C chiller unit. Face the barcode to the right.
13. Select the checkbox for each item, and then select Continue.
Load solutions and reservoirs
At the Deck Setup 2 of 3 stage:
1. Place each of the following reservoirs into its labeled position, fill it with its corresponding reagent, and
cover it with a black CO-RE lid.
The two wells in each reservoir are connected at the base.
2. Place an empty Deionized Water Reservoir into position R5 and fill with 15 mL of deionized water. (For guidance on water quality, see Deionized water quality requirements (page 25).) There is no black CO-RE lid for R5.
The Deionized Water Reservoir reservoir holds the black CO-RE lids during instrument operation.
3. Select the checkbox for each item, and then select Continue.
Load samples, controls, and nanoparticles
At the Deck Setup 3 of 3 stage:
1. Remove the refrigerated reagents from 2 °C to 8 °C storage.
2. Prepare 250–270 μL plasma per sample (16 samples total).
RESERVOIR POSITION REAGENT
Control Dilution Solution Reservoir R1 Control Dilution Solution
Denaturing Solution Reservoir R2 Denaturing Solution
Reduction Solution Reservoir R3 Reduction Solution
Alkylation Solution Reservoir R4 Alkylation Solution
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Chapter 2 Proteograph Assay
Set up the work deck
3. Confirm the centrifuge has reached 4 °C.
4. Centrifuge the 16 samples at 5000 × g for 2 minutes.
5. Transfer each sample to a Seer Sample Tube, which has a barcode label.
– Minimize aspiration of residues that might settle at the bottom of the tubes.
– Avoid aspirating any lipids that collect at the surface of the samples.
– Minimize bubbles forming at the surface of the samples.
6. Record the Sample Tube number (01–16) with the corresponding plasma sample number or other identifier.
7. SetasidetheSampleTubesoniceorat2°Cto8°C.
8. Remove both tube carriers from the autoload tray and place on a workbench.
9. Uncap the Sample Tubes and load them into positions T1–T16 of Tube Carrier 1.
10. Load the Plasma Control tube into position T17 of Tube Carrier 1.
11. Load the MPE Control tube into position T18 of Tube Carrier 1.
12. Confirm that all barcodes in Tube Carrier 1 are visible and return the carrier to the autoload tray.
13. Prepare and load each Nanoparticle tube onto Tube Carrier 2, as follows:
a. Tap NP #1 on the custom table to ensure that the lyo beads are settled and none are stuck on the cap.
b. Uncap NP #1 and load it into position T33 of Tube Carrier 2.
c. Repeat to load the remaining tubes into positions T34–T37.
14. Confirm that all barcodes in Tube Carrier 2 are visible and return the carrier to the autoload tray.
15. Select the checkbox for each item, and then select Continue.
Check labware
1. At the Labware Check stage:
a. Confirm proper loading of the carriers. For a schematic diagram of the loaded work deck, see
Work deck quick reference (page 33).
b. For each of the covered reservoirs, remove its lid, confirm it contains liquid, and replace the lid.
c. Select all checkboxes, and then select Continue.
2. At the Sample Name Dialog stage, enter the name or identification number of each sample.
– To populate all Sample Name fields with values from a .csv file, select Load Sample Names.
– To populate all Sample Name fields with default values, select Default Sample Names.
Default values follow the format _<S#> with sample numbers in ascending order. In a .csv file, the first column lists the Sample Tube number and the second column lists a user-defined sample name. For example: 1S01, … 1S16,.
3. Select Continue.
TIP
You must select every checkbox before continuing.
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Chapter 2 Proteograph Assay Set up the work deck
Scan barcodes and start the method
The barcode reader scans each barcode as a final check to confirm proper work deck setup. During the method, ICS displays each stage with time estimates. For details, see Proteograph Assay processes (page 75).
1. At the Begin Labware Barcoding stage:
a. Confirm proper placements:
– All barcodes face the barcode reader.
– All carriers are pushed to the stop hooks at the back of the autoload tray.
b. Select Continue to scan the barcodes.
2. At the Setup Complete stage:
a. Close the front protective cover.
b. Select Run to start the method.
ICS locks the front protective cover.
WARNING
Do not attempt to open the front protective cover after the method starts. Doing so automatically aborts the method. If you must open the front protective cover, pause the method.
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Chapter 2 Proteograph Assay Clean the instrument
Clean the instrument
1. When the method is complete, ensure that the autoload tray is free from objects and then choose one of the following options:
– Unload Carriers and Run MPE Flush (recommended) — Unload the carriers and automatically start the MPE Flush method, which takes approximately 10 minutes.
– Unload Carriers Only — Unload the carriers without automatically running the MPE Flush method. For instructions on manually starting the method, see Run the MPE Flush method (page 66).
The carriers automatically move from the work deck to the autoload tray.
2. Immediately retrieve the Peptide Collection Plate, which contains the peptides.
3. Seal the plate with an adhesive mat, and then centrifuge at 2000 × g for 30 seconds.
4. Set aside the plate at room temperature. Start peptide quantification within 1 hour. For instructions, see Peptide Quantification method (page 44).
5. Remove labware from the carriers:
a. Remove all plastic labware from the tube, plate, and reservoir carriers.
b. If the MPE module was used for the method, check for and remove the plate.
c. If black CO-RE lids were used for the method, remove them and store for future use.
d. Leave the magnetic plate on the instrument.
6. Dispose of all labware and leftover reagents in the appropriate waste containers per laboratory policy.
7. Turn off the instrument and peripherals.
– SP100 — Press the green switch on the front of the instrument.
– MPE power unit — Press the power button on the front of the MPE power unit.
– Chiller power unit — Press the power switch on the back panel of the chiller power unit.
– Instrument computer — Press the power button on the front of the instrument computer.
8. Proceed to Peptide Quantification method (page 44).
NOTE
Seer recommends shutting down the hardware when it is not in use.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 42

Chapter 3
Peptide Quantification
This chapter provides instructions on how to prepare for and run the Peptide Quantification method on the Seer SP100 Automation Instrument.

Chapter 3 Peptide Quantification Peptide Quantification method
Peptide Quantification method
After you run the Proteograph Assay method, Seer recommends that you quantify the concentration of the peptides in each well of the Peptide Collection Plate. Quantification includes running the Peptide Quantification method and drying the quantified peptides.
To run the Peptide Quantification method, you first prepare materials (see next) and then follow the ICS prompts to set up the work deck. Once the method starts, the instrument automatically performs the steps to convert proteins into peptides.
ProteographTM PQR Labware Kit
The Seer Proteograph PQR Labware Kit (PN S55R1108) provides labware and reagents needed for four Peptide Quantification runs and four Peptide Reconstitution runs on the SP100.
Table 5. Contents of the Seer Proteograph PQR Labware Kit
NOTE
Start quantification within 1 hour of removing the Peptide Collection Plate from the SP100 Automation Instrument. After quantification, you can store the plate for up to 1 year before reconstituting.
DESCRIPTION QUANTITY NOTES
Black Plate Lid 4 1
Cleanup Reagents 4-well Reservoir 4 1
Empty 2 mL Tube 32 1
Intermediate Plate 8 1
Microplate, 96 well, Black 4 1
Peptide Assay Buffer Reservoir 4 1
Peptide Assay Reagent Tube 32 1
Peptide Digest Assay Standard Tube 4 1
Peptide Elution Solution (20 mL) 2 1
Reconstitution Buffer Reservoir 4 2
1For the Peptide Quantification method. 2For the Peptide Reconstitution method.
Additional materials for the Peptide Quantification method
The Peptide Quantification method is designed to work with the ProteographTM PQR Labware Kit (Seer S55R1108) and the PierceTM Quantitative Fluorometric Peptide Assay (Thermo Fisher catalog # 23290; sold separately). Additional materials are listed below. (For supplier information, see Additional required materials (page 24).)
• 300 μL Nested Conductive Tips (NCTs)
• Acid-Resistant CentriVap Centrifugal Vacuum Concentrator (speed vac)
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Chapter 3 Peptide Quantification
Peptide Quantification method
• Aluminum Sealing Foil 5 × 3 Inch
• Personal protective equipment
– Disposable latex gloves
– Lab coats
– Protective goggles
• Pipettes with tips
– 1–10 mL pipette with tips
– 20–200 μL pipette with tips
– 20–200 μL multichannel pipette with tips
– 100–1000 μL pipette with tips
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45

Chapter 3 Peptide Quantification Turn on the instrument
Turn on the instrument
If the SP100 is not already on, use the following instructions to initialize the system and ensure proper communication between the instrument and peripherals.
1. Turn on the following hardware:
– SP100 — Press the green switch on the front of the instrument.
– MPE power unit — Press the power button on the front of the MPE power unit.
– Chiller power unit — Press the power switch on the back panel of the chiller power unit.
– Instrument computer — Press the power button on the front of the instrument computer.
2. Check the gas supply for appropriate pressure.
3. Confirm that the MPE regulator (located near the MPE waste container) is set to > 110 psi.
4. After the computer has initialized, select the Proteograph ICS desktop shortcut to launch ICS.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 46

Chapter 3 Peptide Quantification Prepare the quantification consumables
Prepare the quantification consumables
1. Remove the following room-temperature consumables from the Proteograph PQR Labware Kit:
DESCRIPTION QUANTITY
Black Plate Lid 1
Cleanup Reagents 4-Well Reservoir 1
Empty 2 mL Tube 8
Intermediate Plate 2
Microplate, 96 well, Black 1
Peptide Assay Buffer Reservoir 1
Peptide Assay Reagent Tube 8
Peptide Digest Assay Standard Tube 1
Reconstitution Buffer Reservoir 1
2. Remove the following reagents from 2 °C to 8 °C storage:
– Elution Solution (1 bottle; also part of the Proteograph PQR Labware Kit)
– PierceTM Quantitative Fluorometric Peptide Assay (sold separately)
3. Confirm that the PierceTM Quantitative Fluorometric Peptide Assay includes:
– Fluorometric Peptide Assay Buffer
– Fluorometric Peptide Assay Reagent (4 vials)
– Peptide Digest Assay Standard (1 mg/mL)
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Chapter 3 Peptide Quantification Run the Peptide Quantification method
Run the Peptide Quantification method
1. On the ICS main menu, select Peptide Quantification.
Onscreen prompts guide you through the remaining steps.
2. At the Sign In stage:
a. Enter your username (up to 20 alphanumeric characters, including commas, dashes, periods, spaces, and underscores).
b. Select Continue.
3. At the Tip Counter stage:
a. Check whether enough NCTs are loaded to complete the method.
b. Select Continue.
4. At the Deck Layout stage, prepare reagents as follows and place labware into the indicated position.
INSTRUCTION CARRIER POSITION
Add 150 μL Peptide Digest Assay Standard to the Peptide Digest Standard Tube Carrier 1 T1 tube. Leave the tube uncapped.
Uncap eight Empty Tubes. Leave the tubes empty. Tube Carrier 1 T2–T9
Uncap eight Pep Assay Reagent Tubes and add 310 μL Fluorometric Tube Carrier 1 T11–T18 Peptide Assay Reagent to each tube. Leave the tubes uncapped.
Using a pipette, add 10 mL of Elution Solution into the 4th well. Do not pour Plate Carrier 1 A3 the entire bottle. Return the remainder (if any) to the refrigerator.
Place one Black Quantitation Plate into position A4. Plate Carrier 1 A4
Add 15 mL Fluorometric Peptide Assay Buffer to the Peptide Assay Buffer Reservoir Carrier R4 Reservoir.
Cover one Intermediate Plate with a Black Plate Lid. Plate Carrier 2 B3
Place one Intermediate Plate uncovered in position B4. Plate Carrier 2 B4
If necessary, unseal the Peptide Collection Plate. Plate Carrier 2 B5
Place one stack of NCT racks into position C2. Tip Carrier C2
Place one stack of NCT racks into positions D1 and D2 (one stack of 4 racks Work deck D1–D2 into each).
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Chapter 3 Peptide Quantification Run the Peptide Quantification method
5. At the Labware Check stage:
a. Check that all labware is properly loaded and all carriers are on the autoload tray.
b. Close the front protective cover.
c. Select Continue.
ICS moves the carriers from the autoload tray to the work deck.
The method takes approximately 25–30 minutes to complete.
6. When the method is complete, do the following.
a. Open the front protective cover.
b. Immediately remove the Peptide Collection Plate from position B5 of Plate Carrier 2.
The plate contains the quantified peptides.
c. Remove the Black Plate Lid and seal with an adhesive mat.
7. Clean the work deck and appropriately discard reagents and labware.
8. Dry the peptides:
a. (Optional) Freeze the sealed Peptide Collection Plate at -80 °C for approximately 10 minutes. Then remove it from the freezer.
b. Unseal the plate.
c. Transfer the plate to a concentrator (speed vac).
d. Confirm the concentrator is balanced appropriately.
e. Set the temperature to ≤ 20 °C.
f. Run the concentrator until the peptides are fully dried, which can take several hours.
g. Visually confirm the peptides are fully dried.
9. Proceed depending on when you are reconstituting the peptides:
– If you are reconstituting immediately, proceed to Reconstitute Peptides.
– If you are reconstituting later, seal the Peptide Collection Plate and store at -80 °C for ≤ 1 year.
WARNING
Do not attempt to open the front protective cover after the method starts. Doing so automatically aborts the method. If you must open the front protective cover, pause the method.
TIP
Seer recommends freezing the Peptide Collection Plate to prevent accidental spills while transferring the plate to a concentrator (speed vac).
TIP
Run the concentrator overnight.
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Chapter 3 Peptide Quantification Run the Peptide Quantification method
10. Turn off the instrument and peripherals.
– SP100 — Press the green switch on the front of the instrument.
– MPE power unit — Press the power button on the front of the MPE power unit.
– Chiller power unit — Press the power switch on the back panel of the chiller power unit.
– Instrument computer — Press the power button on the front of the instrument computer.
NOTE
Seer recommends shutting down the hardware when it is not in use.
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Chapter 4
Peptide Reconstitution
This chapter provides instructions on how to prepare for and run the Peptide Reconstitution method on the Seer SP100 Automation Instrument.

Chapter 4 Peptide Reconstitution Peptide Reconstitution method
Peptide Reconstitution method
After the Peptide Quantification method, reconstitute the dried peptides to the concentration and volume needed for MS. Reconstitution includes running the Peptide Reconstitution method to produce MS-ready peptides.
To run the Peptide Reconstitution method, you will prepare materials (see next) and then follow the ICS prompts to set up the work deck. Once the method starts, the instrument automatically performs the steps to reconstitute the peptides.
Additional materials for the Peptide Reconstitution method
The Peptide Reconstitution method is designed to work with the ProteographTM PQR Labware Kit (SeerS55R1108). Additional materials are listed below. (For supplier information, see Additional required materials (page 24).)
• 300 μL Nested Conductive Tips (NCTs)
• Aluminum Sealing Foil 5 × 3 Inch
• Axygen AxyMats 96 Round Well Sealing Mat for PCR Microplates
• Peptide Reconstitution Buffer
• Personal protective equipment
– Disposable latex gloves
– Lab coats
– Protective goggles
• Pipettes with tips
– 1–10 mL pipette with tips
– 20–200 μL multichannel pipette with tips
– 20–200 μL pipette with tips
– 100–1000 μL pipette with tips
Peptide Reconstitution Buffer preparation
Peptides should be reconstituted with a buffer compatible with the LC-MS system that will be used for analysis. If needed, refer to the information provided below to prepare 100 mL of reconstitution buffer.
Equipment
PRODUCT NAME / DESCRIPTION VENDOR / MANUFACTURER CATALOG / PART NUMBER
20-200 uL pipette Rainin or equivalent 17014392 or equivalent
100-1000 uL pipette Rainin or equivalent 17014382 or equivalent
Analogue vortex mixer VWR 444-2791 or equivalent
Microcentrifuge Thermo Fisher 75002451 or equivalent
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Chapter 4 Peptide Reconstitution Peptide Reconstitution method
Reagents and materials
PRODUCT NAME / VENDOR / CATALOG / PART STORAGE DESCRIPTION MANUFACTURER NUMBER TEMPERATURE
20-200 μL, pipette tips Rainin or equivalent GPS-L250 or equivalent +18 °C to +25 °C
100-1000 μL pipette tips Rainin or equivalent GPS-L1000 or equivalent +18 °C to +25 °C
150 mL Polypropylene Storage Corning 430281 or equivalent +18 °C to +25 °C Bottles, Sterile
Acetonitrile (ACN), Mass Spec-grade JT Baker / Fisher 9829-03 / 02-002-174 or +18 °C to +25 °C organic solvent Scientific equivalent
Eppendorf Tubes® 5.0 mL with snap Eppendorf 0030119401 or equivalent +18 °C to +25 °C cap
Formic acid (FA) 98% – 100% EMD Millipore 1.00264.0100 +18 °C to +25 °C
MS Synthetic Peptide Calibration Kit SCIEX 5045759 -20 °C PepCalMix*
Water, HPLC-grade Fisher Chemical or W5-4 or equivalent +18 °C to +25 °C equivalent
*A commercially-available product containing 20 peptides in solution with known mass-to-charge ratios.
Preparation steps
1. Determine the amount of each reagent needed to prepare 100 mL of Peptide Reconstitution Buffer.
2. Prepare the PepCal Diluent as follows:
a. Obtain a 150 mL or appropriate size storage bottle and label with the following information:
– 3% ACN, 0.1% FA, spiked with 5 pmol/mL PepCalMix
– Preparation date
– Operator name / initials
b. Add 96.5 mL of HPLC-grade water, 3 mL of ACN and 100 μL of FA to the bottle.
c. Vortex the bottle for 30 seconds to mix.
3. Prepare the PepCalMix as follows:
CAUTION
Follow all safety, labeling, recordkeeping, and other trained laboratory practices when performing the following procedure. Wear appropriate personal protective equipment (PPE) when operating equipment and handling reagents.
WATER ACN FA PEPCALMIX TOTAL
96.5mL 3mL 100μL 10vials 100mL
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Chapter 4 Peptide Reconstitution Peptide Reconstitution method
a. Obtain the 10 PepCalMix vials from -20 °C freezer. Thaw the vials at room temperature.
b. Add 1 mL of PepCal Diluent in each PepCalMix vial to dilute the peptides.
c. Vortex each PepCalMix vial for 10 to 15 seconds.
d. Place the PepCalMix vials in the microcentrifuge and spin down at 16,000G for 1 minute.
4. Prepare the Peptide Reconstitution Buffer as follows:
a. Remove the PepCalMix vials from the microcentrifuge and spike their entire contents into the
bottle of PepCal Diluent.
b. Vortex the bottle for 30 seconds to mix.
5. Prepare the Eppendorf Tubes as follows:
a. Obtain a sufficient number (approximately 20) of the 5 mL Eppendorf Tubes and label each with
the following information:
– 3% ACN, 0.1% FA, spiked with 5pmol/mL PepCalMix
– Preparation date
– Expiration date (1 year after preparation date)
– Operator name / initials
b. After mixing the solution thoroughly, aliquot the appropriate amount of Peptide Reconstitution Buffer into each 5 mL Eppendorf Tube.
c. Store the prepared aliquots at -80 °C.
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 54

Chapter 4 Peptide Reconstitution Turn on the instrument
Turn on the instrument
If the SP100 is not already on, use the following instructions to initialize the system and ensure proper communication between the instrument and peripherals.
1. Turn on the following hardware:
– SP100 — Press the green switch on the front of the instrument.
– MPE power unit — Press the power button on the front of the MPE power unit.
– Chiller power unit — Press the power switch on the back panel of the chiller power unit.
– Instrument computer — Press the power button on the front of the instrument computer.
2. Check the gas supply for appropriate pressure.
3. Confirm that the MPE regulator (located near the MPE waste container) is set to > 110 psi.
4. After the computer has initialized, select the Proteograph ICS desktop shortcut to launch ICS.
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Chapter 4 Peptide Reconstitution Prepare the files needed for the Peptide Reconstitution method
Prepare the files needed for the Peptide Reconstitution method
The Peptide Reconstitution method requires two files that you will need to prepare before running the method:
• Peptide quant data file – A Microsoft Excel (.xlsx) file, based on a file you obtain from your Seer FAS or support@seer.bio.
• Partial plate map file – A comma-separated values (.csv) file, based on the file generated by the Proteograph Assay method.
ICS will use data from the peptide quant data file to populate columns in the partial plate map file and will then generate a complete plate map file. The complete plate map file will be used as input for post-MS analysis in PAS.
Prepare the peptide quant data file
On a computer other than the instrument computer, do the following. You will need Microsoft Excel.
1. Rename the peptide quant data file by adding _, the Peptide Collection Plate barcode number, and _
data to the end of the filename.
For example: _1LQWERTYU0O2528_data.xlsx
2. Open the file in Excel and modify it as follows:
a. Select the second sheet, which holds the peptide quant data. Rename the sheet (its tab) as Peptide&SeerDB. Leave the other sheets as-is.
b. Locate the cells for the wells that will not need to be reconstituted. In each, enter 0. For example (illustrative purposes only):
c. Save the file and close Excel.
3. Copy the file to portable media such as a USB drive so that you can transfer it to the instrument
computer.
On the instrument computer:
1. Navigate to C:\Users\Publish\Seer\Proteograph\DataFile\Peptide Quant Data File.
2. Copy the peptide quant data file from the portable media to this folder.
NOTE
Before you begin, obtain a copy of the peptide quant data file from your Seer FAS or support@seer.bio.
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Chapter 4 Peptide Reconstitution Prepare the files needed for the Peptide Reconstitution method
Prepare the partial plate map file
On the instrument computer.
1. Navigate to C:\Program Files (x86)\HAMILTON\LogFiles\Method Tracking to locate the plate map file that was generated by the Proteograph Assay method. Copy that file.
2. Navigate to C:\Users\Publish\Seer\Proteograph\DataFile\Partial Plate Map File and paste the partial plate map file there.
3. Rename the partial plate map file by adding _, the Peptide Collection Plate barcode number, and _a to the end of the filename.
For example: _1LQWERTYU0O2528_a.csv
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Chapter 4 Peptide Reconstitution Prepare the reconstitution consumables
Prepare the reconstitution consumables
1. If necessary, remove the Peptide Collection Plate containing the dried, quantified peptides from -80 °C storage and bring to room temperature.
2. Prepare a room-temperature water bath for the Peptide Reconstitution Buffer.
3. Remove the following labware from room-temperature storage:
– 60 mL Reagent Reservoir Self-Standing
– 300 μL NCTs
4. Remove the following reagents from 2 °C to 8 °C storage:
– MS Control
– Peptide Reconstitution Buffer
5. Prepare the Peptide Reconstitution Buffer:
a. Remove from -25 °C to -15 °C storage.
b. Sonicate for approximately 10 seconds in a room-temperature water bath.
c. Vortex briefly.
6. Reconstitute the MS Control:
a. Remove from 2 °C to 8 °C storage.
b. Add 24 μl Peptide Reconstitution Buffer to the MS Control tube.
c. Allow to stand for 1 minute.
d. Gently pipette 10 times to mix.
e. Place on ice and use within the day.
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Chapter 4 Peptide Reconstitution Run the Peptide Reconstitution method
Run the Peptide Reconstitution method
1. On the ICS main menu, select Peptide Reconstitution.
Onscreen prompts guide you through the remaining steps.
2. At the Sign In stage:
a. Enter your username (up to 20 alphanumeric characters, including commas, dashes, periods, spaces, and underscores).
b. Select Continue.
3. At the Start stage, do the following:
a. Verify that the files you prepared earlier are in the expected directories on the instrument computer. (If you have not yet prepared the files, see Prepare the files needed for the Peptide Reconstitution method (page 56) before continuing.)
– Partial plate map file (extension _a.csv) is in C:\Users\Public\Seer\Proteograph\DataFiles\Partial Plate Map File.
– Peptide quant data file (extension _data.xlsx) is in C:\Users\Public\Seer\Proteograph\DataFiles\Peptide Quant Data
File.
b. Select Continue.
4. At the Deck Setup Check stage, load reagents and labware:
a. Add Peptide Reconstitution Buffer to a 60 mL Reagent Reservoir Self-Standing.
b. Place the reservoir into position R1 of the Reservoir Carrier.
c. Place the Peptide Collection Plate into position B5 of Plate Carrier 2.
d. Place one 4-stack of 300 μL NCTs into positions D1 and D2 of the work deck.
e. Select Continue.
5. At the Deck Setup Confirmation stage:
a. Verify that all labware is properly loaded.
b. Select Continue.
6. At the Tip Counter stage:
a. Check for a sufficient number of 300 μL NCTs.
b. Select Continue.
7. At the Volume Verification stage:
a. Check the reconstitution volumes and adjust if necessary. Reconstitution volumes must be within
the range of 0–600 μL.
b. Select Continue.
The method now begins. It will take approximately 20 minutes to complete.
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Chapter 4 Peptide Reconstitution Run the Peptide Reconstitution method
WARNING
Do not attempt to open the front protective cover after the method starts. Doing so automatically aborts the method. If you must open the front protective cover, pause the method.
8. When the method is complete, select End and then open the front protective cover.
9. Remove the Peptide Collection Plate from position B5 of Plate Carrier 2.
10. Add 20 μL reconstituted MS Control to an empty well.
Wells D11–H11 and all wells in column 12 are empty.
11. Seal the Peptide Collection Plate with an MS-compatible seal and store at 2 °C to 8 °C for ≤ 4 days. For longer periods, store at -80 °C.
12. Turn off the instrument and peripherals.
– SP100 — Press the green switch on the front of the instrument.
– MPE power unit — Press the power button on the front of the MPE power unit.
– Chiller power unit — Press the power switch on the back panel of the chiller power unit.
– Instrument computer — Press the power button on the front of the instrument computer.
NOTE
Seer recommends shutting down the hardware when it is not in use.
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Chapter 5 Instrument
Maintenance
This chapter offers procedures and best practices for maintenance of the Seer SP100 Automation Instrument.

Chapter 5 Instrument Maintenance Maintenance methods
Maintenance methods
ICS guides you through the following maintenance methods. The Daily Maintenance and Weekly Maintenance methods are part of normal instrument operation. Perform the MPE Flush and Water Run* methods as needed.
*The Water Run method is accessible on ICS’s Demo and Training Menu.
If an error occurs during a maintenance method, try to resolve the issue and repeat the method. If the issue
persists, contact your Seer FAS or email support@seer.bio. Preventative maintenance
Schedule preventative maintenance, including verification, with a Seer field service engineer (FSE) every six months. A service agreement ensures maintenance and verification at regular intervals.
Materials for maintenance methods
The maintenance methods require the following materials. (For supplier information, see Additional required
materials (page 24).)
• 70% isopropyl alcohol or 70% ethanol
• Personal protective equipment
– Disposable latex gloves
– Lab coats
– Protective goggles
• Waste Bags with Biohazard Labeling
• Waste Container Biohazard Box
APPROXIMATE
ICON METHOD DURATION FREQUENCY
Daily Maintenance
10 minutes Before running the Proteograph Assay method
Weekly Maintenance
30 minutes At the end of each week
MPE Flush 10 minutes
After running the Proteograph Assay method or as needed for troubleshooting
Water Run* 10 minutes During training or troubleshooting with Seer support
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Chapter 5 Instrument Maintenance Run the Daily Maintenance method
Run the Daily Maintenance method
The Daily Maintenance method ensures that waste is emptied and that the pipette heads are holding pressure and pipetting the correct volumes. A series of onscreen prompts guides you through each step.
1. On the ICS main menu, select Maintenance, and then select Daily Maintenance.
2. Inspect the MPE waste container.
a. If the liquid level meets or exceeds the indicator line, empty the container as follows:
i. Press the metal prongs to disconnect the two tubes from the cap.
ii. Unscrew the cap from the container.
iii. Dispose of the contents per laboratory policy.
iv. Screw the cap onto the container and reconnect the tubes.
b. Select the Completed MPE Waste Check checkbox.
c. Select Continue.
3. When prompted to execute daily maintenance, select Yes.
4. Open the front protective cover, and then check whether the deck is clean.
– If the deck is clean, select OK to proceed with daily maintenance.
– If the deck is not clean, select Cancel and perform weekly maintenance instead of daily maintenance.
See Run the Weekly Maintenance method (next page).
5. When prompted to check waste, empty the tip waste, and then select OK.
6. When prompted to execute the channel tightness check, confirm the teaching needles are on the work deck, and then select OK.
ICS displays a series of pop-up windows indicating the status of the channel tightness check.
7. When prompted to execute the channel cLLD check, select OK.
NOTE
Waste is typically located on the custom table under the instrument.
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Chapter 5 Instrument Maintenance Run the Weekly Maintenance method
Run the Weekly Maintenance method
A series of onscreen prompts guides you through the Weekly Maintenance method, which performs the same checks as the Daily Maintenance method plus hardware cleaning. For appropriate cleaning materials, see Hardware cleaning requirements (next page).
1. On the ICS main menu, select Maintenance, and then select Weekly Maintenance.
2. Inspect the MPE waste container.
a. If the liquid level meets or exceeds the indicator line, empty the container as follows:
i. Press the metal prongs to disconnect the two tubes from the cap.
ii. Unscrew the cap from the container.
iii. Dispose of the contents per laboratory policy.
iv. Screw the cap onto the container and reconnect the tubes.
b. Select the Completed MPE Waste Check checkbox.
c. Select Continue.
3. When prompted to execute weekly maintenance, select Yes, and then select OK.
4. Remove all carriers from the autoload tray.
5. Clean the carriers, and then select OK.
6. Open the front protective cover.
7. Clean the work deck, and then select OK.
8. Empty and clean the tip waste container, and then select OK.
9. Clean the glass on the barcode reader with a lint-free cloth or cotton swabs lightly soaked in 70% ethanol.
10. When prompted to execute the channel tightness check, confirm the teaching needles are on the work deck, and then select OK.
ICS displays a series of pop-up windows indicating the status of the channel tightness check.
11. When the method is complete, return the carriers to the autoload tray:
a. Load Tube Carrier 1 in the far left position (track 5).
b. Working left to right, successively load each of the remaining carriers.
NOTE
Waste is typically located on the custom table under the instrument.
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Chapter 5 Instrument Maintenance Run the Weekly Maintenance method
Hardware cleaning requirements
Observe the following requirements for cleaning the instrument hardware.
• Use a cleaning solution of 70% isopropyl alcohol or 70% ethanol as described in the maintenance method instructions.
• Spray the cleaning solution onto a lint-free cloth or Kimwipe, and then wipe down any spills.
CAUTION
Do not use disinfectants that contain hypochlorite or bleach.
Do not use alcohol to clean the acrylic panels. Doing so can damage the finish.
CAUTION
Do not spray cleaning solutions directly inside the work deck.
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Chapter 5 Instrument Maintenance Run the MPE Flush method
Run the MPE Flush method
After running the Proteograph Assay method, ICS prompts you to automatically run the MPE Flush method. Alternatively, you can initiate the method from the Maintenance menu.
1. On the ICS main menu, select Maintenance , and then select MPE Flush.
2. Confirm that all carriers are on the autoload tray.
3. Verify that the MPE filter tray is empty.
4. Load the reagent.
a. Add ~ 200 mL deionized water to the Wash C Solution Single Reservoir.
b. Place the reservoir into position A2.
c. Place one rack of 300 μL NCTs into position B1.
5. Confirm the work deck setup.
a. Leave all carriers on the autoload tray.
b. Select Continue to start the method.
6. When the method is complete:
a. Remove the reservoir and remaining NCTs from the work deck.
b. Select Continue to return to the ICS main menu.
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Chapter 5 Instrument Maintenance Run the Water Run method
Run the Water Run method
The Water Run method uses the same work deck layout as the Proteograph Assay method but replaces the reagents with water.
1. On the ICS main menu, select Demo and Training Materials, and then select Water Run.
2. Follow the onscreen prompts to load the work deck. Replace reagents with the minimum amounts of deionized water as shown below.
DEIONIZED WATER
VOLUME (MINIMUM) POSITION
Sample Tubes 01-16 250 uL T1-T16
Plasma Control 0 uL T17
MPE Control 0 uL T18
Nanoparticle Tubes 0 uL T33 – T37
Wash C Solution Single Reservoir 200 mL A2
Cleanup Reagents 4-Well Reservoir Well 1: 7 mL A3 Well 2: 40 mL
Well 3: 54 mL Well 4: 20 mL
Control Dilution Solution Reservoir 10 mL R1
Denaturing Solution Reservoir 25 mL R2
Reduction Solution Reservoir 7 mL R3
Alkylation Solution Reservoir 7 mL R4
Deionized Water Reservoir 15 mL R5
3. When the method is complete, remove all labware from the work deck.
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Chapter 6 Troubleshooting
This chapter offers troubleshooting guidance for the Seer SP100 Automation Instrument.

Chapter 6 Troubleshooting Resolve error messages
Resolve error messages
ICS guides you through any recoverable failures. If an error persists or the instrument experiences intermediate or critical failures, contact support@seer.bio. Include any error code that ICS displays.
The following sections describe potential error messages displayed during method setup or when a method is running. For help preventing many of these errors, see Best practices (page 30).
Carrier Scan Error
The expected carrier was not found on the autoload tray, and the method cannot continue.
1. Verify that the carrier is seated all the way into the stop hooks.
2. Select Retry.
Cognex Initialization Error
An initialization error appears when ICS cannot connect to the barcode reader. Follow the onscreen instructions listed under the work deck graphic to resolve the error.
If the error persists, turn off the instrument, including the MPE power unit and chiller power unit. Restart the method and try again.
Misaligned labware
ICS pauses the gantry above misaligned labware on the work deck, preventing the method from proceeding.
1. Open the front protective cover.
2. Follow the onscreen prompts to adjust the misaligned labware.
3. Close the front protective cover.
4. Select Repeat.
5. If the error persists and relates to tip pickup, replace the entire NTR.
Lack of pressurized gas or low pressure error
If the MPE power unit or MPE module is not receiving pressurized gas during operation, ICS pauses the method. This error typically occurs during peptide cleanup.
Confirm that the gas pressure of the main supply and the regulator connected to the MPE power unit both read > 110 psi and follow the onscreen prompts. If the error persists, immediately contact Seer at support@seer.bio.
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Chapter 6 Troubleshooting
Resolve error messages
No Barcode Scanned
The barcode scanning error appears when the barcode reader cannot scan a barcode.
1. Select Rescan.
2. If the error persists, perform a manual scan:
a. Open the front protective cover and remove the applicable labware.
b. Select Manual Scan.
c. Enter the barcode number printed on the labware.
d. Return the labware to the work deck. Ensure proper placement.
e. Close the front protective cover.
f. Select Manual Scan.
NTR Scan Error
The NTR scanning error appears when the barcode reader cannot scan an NTR barcode.
1. Adjust the NTR:
a. Open the front protective cover.
b. Remove the NTR.
c. Return the NTR to the work deck. Ensure proper alignment. d. Close the front protective cover.
2. Select Retry.
TIP
If there is no barcode on the labware, contact Seer support at support@seer.bio.
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Chapter 6 Troubleshooting
Pause a method
Pause a method
Pausing a method allows you to resolve an error without aborting the method.
1. On the Running page, select Pause. ICS pauses the method.
2. Open the front protective cover.
3. Adjust labware as indicated in the error message.
4. Close the front protective cover.
5. Select Continue to resume the method.
CAUTION
Resume a paused method as promptly as possible to avoid liquid loss.
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Chapter 6 Troubleshooting
Abort a method
Abort a method
When a method experiences an unresolvable error, you must abort the method.
1. From ICS, select Abort.
2. Select Yes to confirm.
ICS aborts the method and unlocks the protective front cover.
3. Remove labware from the carriers:
a. Remove all plastic labware from the tube, plate, and reservoir carriers.
b. If the MPE module was used for the method, check for and remove the plate.
c. If black CO-RE lids were used for the method, remove them and store for future use.
d. Leave the magnetic plate on the instrument.
4. Dispose of all labware, plasma samples, and leftover reagents in the appropriate waste containers per laboratory policy.
CAUTION
Aborting a method is final. ICS cannot resume the method and consumables cannot be reused.
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Chapter 6 Troubleshooting Package trace files
Package trace files
If you encounter a support issue and must send documentation to Seer, use the following instructions to package the necessary trace files.
On the desktop of the instrument computer, double-click Seer Support Package Creator.
1. In the dialog, specify an output location for the trace files.
2. The software places a .zip file in the specified location.
3. Send the .zip file to support@seer.bio.
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Appendix A Automation
This appendix offers a detailed breakdown of each step in the Proteograph Assay method.

Appendix A Automation Proteograph Assay processes
Proteograph Assay processes
After starting the Proteograph Assay method, the SP100 Automation Instrument performs the following automated steps. The total run time is approximately 7 hours and 17 minutes.
For a summary of these steps, including their individual durations and cumulative duration, see Proteograph Assay steps (page 9).
DURATION STAGE # STAGE NAME STEPS (MINUTES)
1 Sample Dispensing A. Transfer Samples to Sample Prep Plate 5 B. Transfer Plasma Control to Sample Prep Plate
2 Nanoparticle Transfer
A. Move Consumables 24 B. Aliquot Nanoparticles
C. Transfer Control Nanoparticle to Intermediate Plate
D. Transfer Nanoparticles to Sample Prep Plate E. Transfer Used Tip Rack
3 Protein Corona: Formation A. Move Sample Prep Plate 60 B. Move Sample Prep Plate Lid
C. Incubate Sample Prep Plate
4 Protein Corona: Washing
A. Move Sample Prep Plate Lid Off 36 B. Remove Supernatant
C. Transfer Used Tip Rack
D. Add Wash Buffer
E. Transfer Used Tip Rack F. Remove Supernatant G. Transfer Used Tip Rack H. Add Wash Buffer
I. Transfer Used Tip Rack J. Remove Supernatant K. Transfer Used Tip Rack L. Add Wash Buffer
M. Transfer Used Tip Rack
N. Prepare Digestion Control
O. Transfer Digestion Control To Sample Prep Plate P. Move Wash Buffer Lid On
5 Protein Corona Denaturation: A. Add Denaturing Solution to Sample Prep Plate 9
Preparation
B. Add Reduction Solution to Sample Prep Plate C. Add Alkylation Solution to Sample Prep Plate
6 Protein Corona Denaturation: A. Move Sample Prep Plate to Heater Shaker 31
Incubation
B. Incubation
C. Move Sample Prep Plate Lid Off D. Cool Down
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Appendix A Automation Proteograph Assay processes
DURATION STAGE # STAGE NAME STEPS (MINUTES)
7 Protein Digestion: Preparation A. Move Sample Prep Plate Lid Off 3 B. Add Trypsin/Lys-C
8 Protein Digestion: Incubation A. Move Sample Prep Plate to Heater Shaker 181 B. Incubate Sample Prep Plate
C. Move Sample Prep Plate Lid Off
9 Protein Digestion: Stop
A. Move Cleanup Reagents 4-Well Reservoir Lid 9 Off
B. Add Digestion Stop Solution
C. Move Cleanup Reagents 4-Well Reservoir Lid
On
D. Transfer MPE Control to Sample Prep Plate E. Move Consumables
F. Prepare Peptides for Cleanup
10 Peptide Addition to Peptide A. Transfer contents of Sample Prep Plate to 12 Cleanup Plate Peptide Cleanup Plate
11 Peptide Wash A A. Add Wash A from Intermediate Plate to Peptide 10 Cleanup Plate
12 Peptide Wash B (1 of 3) A. Add Wash B from Intermediate Plate to Peptide 6 Cleanup Plate (1 of 3)
13 Peptide Wash B (2 of 3) A. Add Wash B from Intermediate Plate to Peptide 6 Cleanup Plate (2 of 3)
14 Peptide Wash B (3 of 3) A. Add Wash B from Intermediate Plate to Peptide 6 Cleanup Plate (3 of 3)
15 Peptide Elution A. Move Peptide Collection Plate 7 B. Add Elution Solution to Peptide Cleanup Plate
16 Finalization (Method A. Move Cleanup Reagents 4-Well Reservoir Lid 2 Completion) On
B. Write Files
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Appendix B
Safety and Compliance
This appendix provides safety and regulatory compliance information for the proper use of the Seer SP100 Automation Instrument.

Appendix B Safety and Compliance Safety considerations and markings
Safety considerations and markings
This appendix describes the primary safety hazards, including the safety symbols affixed to the instrument, and regulatory and compliance information. To ensure safe and correct instrument operation, review this information before operating or maintaining the SP100 Automation Instrument.
• For complete environmental, health, and safety information, refer to the safety data sheets (SDS) provided in the Training Kit.
• For instrument specifications and lab requirements, including installation information, see the SP100 Automation Instrument Site Prep Guide (CF-1017 B).
Intended use
The Seer SP100 Automation Instrument is a robotic liquid handling workstation classified as a general laboratory instrument for research use only (RUO), and not as an in vitro diagnostic (IVD) device. The SP100 is intended to automate routine pipetting tasks and the transportation of plates, tips, and other labware.
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Appendix B Safety and Compliance Instrument operation
Instrument operation
Only trained service personnel can install the instrument, and the instrument operator must attend Seer training. The procedures described in this guide are tested and optimized, so any deviation can compromise results or cause malfunction.
Always wear appropriate protective clothing, goggles, and gloves when operating the instrument or conducting maintenance. During routine operation, shield the instrument from direct sunlight and intense artificial light. Stand clear of all moving parts and the work deck. Do not lean over or into the instrument.
Emergency shutoff
Press the green switch on the front of the instrument to turn off the SP100. If at risk of electric shock, also unplug the instrument.
CAUTION
To avoid personal injury and/or equipment damage, never attempt to lift or move an installed instrument.
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Appendix B Safety and Compliance
Safety hazards
Safety hazards
The following symbols identify safety hazards to consider when operating the instrument.
Table 6. Safety hazard symbols
Laser beam
The barcode reader has a Class II Laser Diode. Do not stare into the beam.
LOCATION ON SYMBOL DESCRIPTION INSTRUMENT
Power Connection – Connect only to an earth-grounded outlet. Left side of
Laser Beam (Autoload) – Do not stare into the beam of the class 2 laser of the barcode reader.
exterior
Connection to PC – Use only the appropriate shielded cables.
USB Connection – Exceeding a cable distance of 5 m can cause signal loss. Pipetting Arm – Do not manually move the pipetting arm.
Moving Parts – Do not open the protective front cover during a method. A moving arm resides in the instrument so opening the cover aborts the method.
CO-RE head Gantry
Stop hooks
Biohazard Warning – The deck and waste might contain biohazardous chemicals. Do not touch biohazardous materials. The instrument drops used tips into a waste container emptied during daily maintenance or when full.
Chiller
CO-RE head Work deck Heater shaker Magnetic plate MPE
Waste
Hot Surface – Avoid contact with the heater shaker, which has hot surfaces that can Heater shaker cause injury if touched.
Pinch Point – Keep fingers and hands clear of the area. Mechanical moving parts can CO-RE head
injure fingers and hands.
Gantry
Magnetic Field – Note that the magnetic plate generates a magnetic field. Incorrect use Magnetic plate can harm the operator.
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Appendix B Safety and Compliance Safety hazards
Electromagnetic radio frequency
The SP100 conforms to European norms for interference immunity. However, exposure to electromagnetic radio frequency (RF) fields or the discharge of static electricity directly onto the instrument can negatively impact function. Keep the instrument away from equipment that emits electromagnetic RF fields and minimize static electricity in the immediate vicinity.
Electrostatic charge
When handling labware and tips, avoid any electrostatic charge. Electrostatic charge can damage the instrument and impact labware stability.
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Appendix B Safety and Compliance Regulatory compliance
Regulatory compliance
The SP100 is designed, tested, and certified for compliance with the standards listed in the following table.
Product certification
The instrument is certified to the following standards.
STANDARD DESCRIPTION
IEC/EN 61010-1:2010 Safety Requirements for Electrical Equipment for Measurement, Control, and (3rd Edition) Laboratory use.
EN 61326-1:2013 Electrical Equipment for Measurement, Control and Laboratory Use. EMC Requirements.
EN 61326-2-6 Specifies minimum requirements for immunity and emissions regarding electromagnetic compatibility for in vitro diagnostic medical equipment, taking into
account the particularities and specific aspects of this electrical equipment and their electromagnetic environment.
EN 61000-3-2 Electromagnetic compatibility (EMC) – Part 3-2: Limits – Limits for harmonic current emissions (equipment input current ≤ 16 A per phase).
EN 61000-3-3 Electromagnetic compatibility (EMC) – Part 3-3: Limits – Limitation of voltage changes, voltage fluctuations and flicker in public low-voltage supply systems, for
equipment with rated current ≤ 16 A per phase and not subject to conditional connection.
CSA C/US mark
CE Mark
RoHS directive
The CSA C/US mark signifies that the product is certified for both US and Canadian markets to the applicable US and Canadian standards.
The CE Mark indicates that assembly is covered by a Declaration of Conformity and has been declared in conformity with the provisions of all applicable directives in the European Union (EU).
RoHS Directive (2011/65/EU): Restriction of the use of certain hazardous substances in electrical and electronic equipment
WEEE Directive (2012/19/EU): Waste Electrical and Electronic Equipment
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Appendix B Safety and Compliance Regulatory compliance
FCC compliance
This device complies with part 15 of the FCC Rules. Operation is subject to the following two conditions: (1) This device may not cause harmful interference, and (2) this device must accept any interference received, including interference that may cause undesired operation.
NOTE
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense.
Conformité IC
ICES-003 (Canada): This Class A digital apparatus complies with Canadian ICES-003. Cet appareil numérique de la classe A est conforme à la norme NMB-003 du Canada.
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Glossary AI
ACN
Acetonitrile.
C
case
Holds six sleeves of stacks, for a total of 120 NTRs holding 11,520 NCTs.
CO-RE
Compressed O-ring expansion.
consumables
Reagents and plasticware.
custom file
ICS
L
LC
LC-MS
Liquid chromatography mass spectrometry.
M
materials
Consumables and equipment.
MPE
Monitored multi-flow positive pressure evaporative extraction.
MPE Control
Reference peptides added before desalting cleanup.
MS
Mass spectrometry.
MS data file
The results of MS analysis for each sample or control in a plate in a .raw, .wiff, .wiff.scan file.
MS Control
Reference peptides added before LC-MS analysis.
N
NCT
Nested conductive tips.
Abbreviation of ProteographTM Instrument Control Software.
Liquid chromatography.
Optional sample information in a .csv, .tsv, .xls, or .xlsx file.
Digestion Control
D
A reference sample added before nanoparticle incubation.
E
equipment
Reusable laboratory equipment.
F
FA
Formic acid.
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Glossary
NP
ProteographTM Instrument Control Software
Software onboard the SP100 used to operate the instrument.
ProteographTM PQR Labware Kit
A Seer kit containing labware and reagents needed for four Peptide Quantification runs and four Peptide Reconstitution runs on the SP100.
ProteographTM Product Suite
The bundle of Seer kits, instrument, and analysis software.
Q
QC
R
Nanoparticle.
NTR
Nested tip rack. See also rack.
pallet
Holds 32 cases of sleeves, for a total of 3,360 NTRs holding 322,560 NCTs.
partial plate map file
A comma-separated values (.csv) file, based on the file generated by the Proteograph Assay method.
PAS
Short name of ProteographTM Analysis Suite.
peptide quant data file
P
A Microsoft Excel (.xlsx) file, based on a file you obtain from your Seer FAS or support@seer.com.
rack
Holds 96 NCTs. Also called a nested tip rack (NTR).
S
sleeve
Holds five stacks of NTR racks, for a total of 20 racks holding 1,920 NCTs.
SP100 Automation Instrument
The Seer liquid handling instrument.
stack
Holds four NTRs, for a total of 384 NCTs.
plate (labware)
A piece of labware containing 96 wells where various steps of the assay are performed. Types of plates used in the Proteograph Assay include intermediate (Nunc) plates, sample prep plate, peptide cleanup plate, and peptide collection plate.
plate map file
The location of each sample in a plate in a .csv file. Used when analyzing MS data in PAS and for automated peptide reconstitution on the SP100.
PQR
Peptide quantification and reconstitution.
Process Control
A reference sample added before nanoparticle incubation.
ProteographTM Analysis Suite
Seer software used to process, analyze, and visualize LC-MS data.
ProteographTM Assay Kit
A Seer kit containing the reagents and labware for preparing samples on the SP100.
Quality control.
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Index
A
abort function 11, 41, 80 adjustable arm 10 alcohol 65
Alpaqua Magnum FLX 17 artificial light 79
assays
peptide preparation 22, 28 quantification 24
automated stages 28 automated steps 28, 75
B
barcode labels 14, 30, 41, 70 barcode reader 80
cleaning 64
errors 69
scanning 14, 30, 70
best practices 28, 30, 65 biohazards 19, 80
bubbles, minimizing 39
buffer, peptide reconstitution 52 buffers 8, 22
bumpers, autoload tray 11 C
cables 80
cap colors 22
Carrier Scan Error 69 carriers 11
cleaning 64 loading 30 types 12, 14, 38
catalog numbers 24
centrifuge temperature 35 certifications 13, 82
channel cLLD 63-64
channel tightness 63-64
chemicals 80
chiller unit 10, 12, 15, 34, 42, 46, 55, 80
errors 69
temperature 35 cleaners 65
clear bags, waste 19
CO-RE head 15-16, 19, 80 Cognex Initialization Error 69 compliance 78, 81, 83 consumables 24
contact information, Seer 62, 89 controls 22, 39
reconstituting 35, 58
storing 22, 35 coronas 17, 28, 75 critical failures 69, 72 custom table 10, 63-64 customer support 89
D
daily maintenance 19, 21, 34, 62, 80 data management 10 DeckSetup1of3 38 DeckSetup3of339
deck setup stages 38-39 Declaration of Conformity 82 deionized water 25, 66-67 denaturing samples 16, 28, 75 Device Initialization 36 digestion controls 28 directories 56
disinfectants 65 disposal 42 downloading data 10 droplets 38-39 drying peptides 44 durations 9, 28, 62, 75
E
electromagnetic compatibility 82 elution 28, 75
EMC requirements 82
empty wells 29
emptying waste 63-64 environment 78 equipment 24
Error Messages 69 errors 30, 69, 72 ethanol 65
experiment information 36 Experiment Registration 36
F
failures 69 files 52
formats 56
naming 56
partial plate map file 56 troubleshooting 73
G
gantry 15, 17, 69, 80
gas supply 34, 46, 55, 69 gloves 24, 79
goggles 24, 79 grounded earth 80
H
Hamilton software 11 hardware 10-11, 18, 64 health information 78 heater shaker 12, 80 help, technical 89
hot surfaces 16, 80 I
ICS 8, 11, 34, 46, 55, 62, 69 ICS menus 20 initialization 34, 36, 46, 55 inputs 28
installation 78 instrument
certifications 82 classification 78
cleaning 64-65
exterior components 10-11 lifting 78
model number 13 moving 78 specifications 10, 78 turning off 42, 79
instrument computer 10, 34, 42, 46, 55, 73 intermediate failures 69
Intermediate Plates 38
IVD use 78
K
kit box 22 kits
assay 22
PQR labware 44 kits, quantification 24
L
lab coats 24, 79
lab policies 42, 63-64, 72
fill volumes 22
filter plate 18, 66
filter tray 18, 66
front protective cover, unlocking 41, 71-72
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY
86

Index
lab requirements 10, 24, 78, 81 labels 13, 22, 78, 80, 82 labware 22, 44
barcode labels 14, 30, 39 disposal 42, 63-64, 72 errors 69
placement 12, 30, 33 reusing 72
scanning 70 static 81 storing 22
laser beams 80
leftover reagents 72
lid types 23
lifting 78
liquid handling 15, 17, 78 load labware
barcode labels 35 lock out, tag out 79
M
magnetic fields 80
magnetic plate 12, 72, 80
main menu 20, 34, 36, 46, 55 maintenance 8, 19, 21, 24, 62, 79 maintenance menu 20, 66 manual scans 70
mass spectrometry 8, 28 materials 28, 44, 52, 62
quantification 47
reconstitution 58 methods
aborting 11, 80 durations 62 pausing 11, 69 resuming 71 stages 28, 75 types 21, 62
Microlab STAR software 11 mixing 16
model number 13
monitor 10-11
moving 78
moving parts 79-80
MPE 12, 19, 34, 42, 46, 55, 69, 80
cleaning 66
filter tray 66 MPE control 10 MPE controls 28 MPE flush 62
MPE flushes 42, 62 MPE module 18
filter tray 18
MPE power unit 18
MPE regulator 34, 46, 55 MPE unit
errors 69
nameplate 13
nanoparticles 8, 17, 22, 29 preparing 39 transferring 28, 75
Nested Tip Track 70
No Barcode Scanned 70 NTR Scan Error 70 number of samples 8, 39
O
optional methods 21 outputs 29, 42
P
part numbers 24
partial plate map file 56-57 pausing 11, 69
Peptide Cleanup Plate 18, 38, 72 Peptide Collection Plate
barcode number 56 contents 29 loading 38
storage 44, 52 unloading 42
peptide quant data filefiles peptide quant data file 56
Peptide Quantification 44
peptide quantification file 52 Peptide Quantification method 44 Peptide Reconstitution 52 peptide reconstitution buffer 52 Peptide Reconstitution method 52 peptides 8
quantification 21 reconstitution 21 transferring 17
peripherals 10, 15, 18, 34, 42, 46, 55 pinch points 80
pipette heads 16, 18-19, 63-64 pipetting 13, 38
pipetting arm 80
pipetting best practices 30 plasma 35, 39, 72
plate grippers 32
plate map 28-29
plate types 23
portable devices 10, 56 power 18, 34, 42, 46, 55 power connections 10, 79-80 PPE 24, 79
prerequisites 28
pressure 19, 63-64
process controls 28 products 8
protein coronas 28, 75 Proteograph Assay 28 Proteograph Assay method
automated steps 9, 28, 75 input 28
output 29, 42 prerequisites 28
work deck layout 33
Proteograph workflow 8 proteomics 8
protocols 9, 28, 44, 52
Q
quality control 8 quantification 21, 44
R
reagents 8, 22, 44 cap colors 22 disposal 42 labels 22 placement 30, 33 reusing 72 storing 22, 47, 58
reconstitution 21, 35 reconstitution buffer 24, 58 red bags, waste 19 refrigerated box 22 regulator 69
regulatory information 78 rescanning 70
Research Use Only 78 resuming 71
reusing consumables 72 RF fields 81, 83
run times 75
RUO use 78
S
safety
hazards 78, 80 information 13, 78 standards 82 symbols 78, 80
Sample Prep Plate 16, 38 Sample Tubes 23, 39-40 samples
denaturing 16 naming 40 number of 8 plate locations 29
seals 24
Seer contact information 62, 89 Seer Support Package Creator 11, 73 shielded cables 80
Sign In 36, 48, 59
site prep 10, 24, 78
slide blocks 11
sonication 39
specifications 10, 78
speed vac 24
static electricity 81
stop hooks 11, 30, 80
sunlight 79
symbols 78, 80
N
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY
87

Index
T
technical assistance 89 temperature control 15-16 temperatures
centrifuge 35 chiller unit 35 storage 35
tip waste 64 tips
counting 36 handling 81 loading 12, 38 pickup 69 replenishing 36 waste 19
touchscreen 10-11 trace files 11
tracks, autoload tray 11 training 21, 62
trap column 26 troubleshooting 8, 21, 30, 62 troubleshooting files 11, 73 trypsin 15, 22, 35, 38
turning off 79
turning on 34, 46, 55
U
unlocking 71-72
uploading data 10
USB ports 10, 56 user-supplied consumables 24 user-supplied equipment 24 user interface 10, 20
user name 36 V
verification 62 visualization 8
W
wash solutions 38 washes 28, 42, 75 waste 13, 18, 72, 80, 82
emptying 63-64
water baths 35, 39
Water Run method 67 water runs 62
WEEE Directive 82 weekly maintenance 21, 62 work deck 30
cleaning 64 layout 33 loading 35 safety 79-80 setup 38-39
work surfaces 11
workflows 8-9, 22
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 88

Technical Support
For technical assistance, contact Seer.
Contact Information
Seer, Inc.
3800 Bridge Pkwy #102 Redwood City, CA 94065 Email: support@seer.bio
seer.bio
Telephone
650.453.0000
Proteograph Product Suite User Guide (CF-1016 A) – FOR FIELD TESTING USE ONLY 89

Seer, Inc.
3800 Bridge Pkwy #102 Redwood City, CA 94065 650.453.0000 info@seer.bio
seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1111
Product name: Denaturing Solution
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
SECTION 2: Hazards identification
GHS – Classification Signal Word
Not Hazardous
Hazard pictograms
Not Applicable
Health hazards
Not Hazardous
Physical hazards
Not Hazardous
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 1 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

Environmental hazards
Not Hazardous
Precautionary Statements Prevention
Not Applicable
Response
Not Applicable
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
Health 0 Flammability 0 Reactivity 0
SECTION 3: Composition/information on ingredients
The product contains no substances which at their given concentration, are considered to be hazardous to health.
Description of first aid measures Skin contact
Eye contact
Ingestion Inhalation
SECTION 4: First aid measures
Rinse with plenty of water . Immediate medical attention is not required.
Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice.
Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary.
Treat symptomatically.
Notes to Physician
Most important symptoms and effects, both acute and delayed
Indication of any immediate medical attention and special treatment needed
None.
SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable
extinguishing media No information available.
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

Special hazards arising from the substance or mixture Advice for fire-fighters
Standard procedure for chemical fires
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Always wear recommended Personal Protective Equipment. Use personal protection equipment See Section 8 for more detail.
Environmental precautions
No special environmental precautions required. .
Methods and material for containment and cleaning up
Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
Precautions for safe handling
SECTION 7: Handling and storage
Use personal protective equipment as required. No special handling advices are necessary.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers.
Specific end use(s)
For research use only.
SECTION 8: Exposure controls/personal protection
Control parameters
Exposure Limits Contains no substances with occupational exposure limit values.
Engineering measures Ensure adequate ventilation, especially in confined areas. Exposure controls
Personal Protective Equipment
Respiratory protection
Hand protection Eye protection
In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Wear suitable gloves. Glove material: Compatible chemical-resistant gloves. Tight sealing safety goggles.
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 3 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

Skin and Body Protection Wear suitable protective clothing.
Hygiene Measures Handle in accordance with good industrial hygiene and safety practice
Environmental exposure controls
No special environmental precautions required. .
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties
Appearance Odor
pH
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate
Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Explosive properties
Other information
No data available.
Reactivity Chemical stability
Possibility of hazardous reactions
Conditions to avoid Incompatible materials
liquid
slight amine
7-9
°C Mixture has not been tested
°C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available
No data available
Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available
No data available
No data available
Mixture has not been tested
SECTION 10: Stability and reactivity
None known.
°F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested
Stable under normal conditions. Hazardous reaction has not been reported.
No information available.
No dangerous reaction known under conditions of normal use.
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 4 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

Hazardous decomposition products
No data available.
SECTION 11: Toxicological information
Information on toxicological effects
There is no evidence available indicating acute toxicity.
Principal Routes of Exposure Irritation
Corrosivity
Sensitization
STOT – Single Exposure STOT – Repeated Exposure Carcinogenicity Mutagenicity
Reproductive toxicity Aspiration hazard
Toxicity
Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification
Conclusive but not sufficient for classification Conclusive but not sufficient for classification
SECTION 12: Ecological information
The environmental impact of this product has not been fully investigated.
Persistence and degradability No information available. Bioaccumulative potential No information available.
Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available.
SECTION 13: Disposal considerations
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations.
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not classified as dangerous in the meaning of transport regulations.
UN number Not Applicable
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

UN proper shipping name Transport hazard class(es) Packing group
Environmental hazards
Not Applicable
Special precautions for user
Not Applicable
Not Applicable Not Applicable Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code
Not Applicable.
US Federal Regulations SARA 313
This product is not regulated by SARA.
SECTION 15: Regulatory information
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contains HAPs.
US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
Non-controlled
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Not regulated
Reason for revision
Revision number 2
SECTION 16: Other information
Revision date 23-Nov-2021
Use as laboratory reagent. Scientific research and development.
References
• ECHA: http://echa.europa.eu/
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 7 Product code S55R1111 Product name Denaturing Solution www.seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1112
Product name: Digestion Stop Solution
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
SECTION 2: Hazards identification
GHS – Classification Signal Word
WARNING
Hazard pictograms
Health hazards
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 1 / 8 Product code S55R1112 Product name Digestion Stop Solution
www.seer.bio

Skin corrosion/irritation
Serious eye damage/eye irritation
Physical hazards
Not Hazardous
Environmental hazards
Not Hazardous
Hazard Statements
H315 – Causes skin irritation
H319 – Causes serious eye irritation
Precautionary Statements
Prevention
P264 – Wash hands thoroughly after handling
P280 – Wear protective gloves/protective clothing/eye protection/face protection
Response
Category 2 Category 2
P302 + P352 – IF ON SKIN: Wash with plenty of soap and water
P305 + P351 + P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing
P332 + P313 – If skin irritation occurs: Get medical advice/attention
P337 + P313 – If eye irritation persists: Get medical advice/attention
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
Health 2 Flammability 0 Reactivity 0
SECTION 3: Composition/information on ingredients
Component
CAS-No
EINECS- No
Formic acid 64- 18-6 ( 2-10 )
64-18-6 200-579-1 2-10
Weight %
We recommend handling all chemicals with caution.
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 8 Product code S55R1112 Product name Digestion Stop Solution
www.seer.bio

SECTION 4: First aid measures
Description of first aid measures Skin contact
Eye contact Ingestion Inhalation
Notes to Physician
Most important symptoms and effects, both acute and delayed H315 – Causes skin irritation H319 – Causes serious eye irritation
Indication of any immediate medical attention and special treatment needed
None.
SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable
extinguishing media No information available. Special hazards arising from the substance or mixture
Not known
Advice for fire-fighters
Wear self-contained breathing apparatus and protective suit
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Avoid contact with skin, eyes or clothing Use personal protection equipment See Section 8 for more detail.
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up
Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use. Immediate medical attention is required.
Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required.
Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur.
Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician.
Treat symptomatically.
Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
Precautions for safe handling
SECTION 7: Handling and storage
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 3 / 8 Product code S55R1112 Product name Digestion Stop Solution
www.seer.bio

Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations.
Specific end use(s)
Use as laboratory reagent. Scientific research and development.
SECTION 8: Exposure controls/personal protection
Control parameters
Chemical Name
Formic acid
Chemical Name
Formic acid Engineering measures
5 ppm None 9 mg/m3
10 ppm
None
OSHA PEL
OSHA PEL (Ceiling)
ACGIH OEL (TWA)
ACGIH OEL (STEL)
5 ppm
None
Ensure adequate ventilation, especially in confined areas.
Brazil – OEL – TWAs (LTs)
Brazil – OEL – Ceilings
Brazil – OEL – Skin Designations
4 ppm 7 mg/m3
Exposure controls
Personal Protective Equipment
Respiratory protection Hand protection
Eye protection
Skin and Body Protection
Hygiene Measures
In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Glove material:. Nitrile rubber. with thickness (mm). :5. Break through time. (hours). :1.
Recommended glove type has not been tested for use with product. Information is based on professional Knowledge.
Tight sealing safety goggles.
Wear laboratory coat for body protection.
Handle in accordance with good industrial hygiene and safety practice
Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties Appearance liquid
Odor Mixture has not been tested
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 4 / 8 Product code S55R1112 Product name Digestion Stop Solution
www.seer.bio

Odor Threshold
pH
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate
Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Viscosity
Explosive properties
Oxidizing properties
Other information
No data available.
Reactivity Chemical stability
Possibility of hazardous reactions
Conditions to avoid Incompatible materials
Hazardous decomposition products
Mixture has not been tested
<3 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Mixture has not been tested No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested SECTION 10: Stability and reactivity °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested None known. Stable under normal conditions. Hazardous reaction has not been reported. No information available. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. SECTION 11: Toxicological information Information on toxicological effects Formic acid = 1100 mg/kg (Rat) No data available =15g/m3(Rat) ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 8 Product code S55R1112 Product name Digestion Stop Solution Chemical Name LD50 (oral,rat/mouse) LD50 (dermal,rat/rabbit) LC50 (inhalation,rat/mouse) www.seer.bio Principal Routes of Exposure Irritation Corrosivity Sensitization STOT – Single Exposure STOT – Repeated Exposure Carcinogenicity Mutagenicity Reproductive toxicity Aspiration hazard Toxicity Skin irritation Irritating to eyes Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification SECTION 12: Ecological information The environmental impact of this product has not been fully investigated. Chemical Name Freshwater Algae Water Flea Data Freshwater Fish Microtox Data log Pow Data Species Data Persistence and degradability No information available. Bioaccumulative potential No information available. Results of PBT and vPvB assessment This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available. SECTION 13: Disposal considerations Waste treatment methods The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations. SECTION 14: Transport information IATA / ADR / DOT-US / IMDG Not classified as dangerous in the meaning of transport regulations. UN number Not Applicable UN proper shipping name Not Applicable ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 8 Product code S55R1112 Product name Digestion Stop Solution Formic acid Desmodesmus subspicatus EC50=25 mg/L (96 h) Desmodesmus subspicatus EC50=26.9 mg/L (72 h) Daphnia magna EC50=120 mg/L (48 h) Daphnia magna EC50138 – 165.6 mg/L (48 h) No data available No data available logPow-0.54 www.seer.bio Transport hazard class(es) Packing group Environmental hazards Not Applicable Special precautions for user Not Applicable Not Applicable Not Applicable Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable. SECTION 15: Regulatory information Formic acid 64- 18-6 ( 2-10 ) Listed Component US TSCA US Federal Regulations SARA 313 This product contains the following toxic chemical(s) subject to the notification requirements of section 313 of Title III of the Superfund Amendments and Reauthorization Act of 1986. This law requires certain manufacturers to report on annual emissions of specified chemicals and chemical categories. Please note that if you repackage, or otherwise redistribute, this product to industrial customers, a notice similar to this one should be sent to those customers. Chemical Name CAS-No Weight % Formic acid 64-18-6 2-10 1.0 Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61) This product does not contains HAPs. US State Regulations California Proposition 65 This product does not contain any Proposition 65 chemicals. WHMIS Hazard Class D2B – Toxic materials SARA 313 – Threshold Values This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR. National Regulations – Brazil Formic acid 64-18-6 Not Listed Not Listed ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 8 Product code S55R1112 Product name Digestion Stop Solution Chemical Name CAS-No Brazil – National Agency for Sanitary Surveillance (ANVISA) Brazil – National List of Carcinogen Agents to Humans (LINACH) www.seer.bio SECTION 16: Other information Reason for revision Revision number 2 Revision date 23-Nov-2021 Use as laboratory reagent. Scientific research and development. References • ECHA: http://echa.europa.eu/ • TOXNET: http://toxnet.nlm.nih.gov/ • eChemPortal: http://www.echemportal.org/ • LOLI database: https://www.chemadvisor.com/loli-database “The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE” End of Safety Data Sheet ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 8 / 8 Product code S55R1112 Product name Digestion Stop Solution www.seer.bio Safety Data Sheet SECTION 1: Identification of the substance/mixture and of the company/undertaking Identification of the substance or mixture Product code: S55R1113 Product name: Enzyme Reconstitution Solution Company/undertaking identification Name: Seer, Inc. Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000 24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC: Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970 For Research Use Only. Not for use in diagnostic procedures. SECTION 2: Hazards identification GHS – Classification Signal Word Not Hazardous Hazard pictograms Not Applicable Health hazards Not Hazardous Physical hazards Not Hazardous __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 1 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio Environmental hazards Not Hazardous Precautionary Statements Prevention Not Applicable Response Not Applicable Storage Not Applicable Disposal Not Applicable Other hazards Not Applicable HMIS Health 0 Flammability 0 Reactivity 0 SECTION 3: Composition/information on ingredients The product contains no substances which at their given concentration, are considered to be hazardous to health. Description of first aid measures Skin contact Eye contact Ingestion Inhalation SECTION 4: First aid measures Rinse with plenty of water. Immediate medical attention is not required. Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing. Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice. Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary. Treat symptomatically. Notes to Physician Most important symptoms and effects, both acute and delayed Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures Extinguishing media Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available. __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 2 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio Special hazards arising from the substance or mixture Advice for fire-fighters Standard procedure for chemical fires SECTION 6: Accidental release measures Personal precautions, protective equipment and emergency procedures Ensure adequate ventilation Always wear recommended Personal Protective Equipment Use personal protection equipment See Section 8 for more detail Environmental precautions No special environmental precautions required. . Methods and material for containment and cleaning up Soak up with inert absorbent material. Reference to other sections See section 8 for more information. Precautions for safe handling SECTION 7: Handling and storage Use personal protective equipment as required. No special handling advices are necessary. Conditions for safe storage, including any incompatibilities Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Specific end use(s) For research use only. SECTION 8: Exposure controls/personal protection Control parameters Exposure Limits Contains no substances with occupational exposure limit values. Engineering measures Ensure adequate ventilation, especially in confined areas. Exposure controls Personal Protective Equipment Respiratory protection Hand protection Eye protection In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards. Wear suitable gloves. Glove material: Compatible chemical-resistant gloves. Tight sealing safety goggles. __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 3 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio Skin and Body Protection Wear suitable protective clothing. Hygiene Measures Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls No special environmental precautions required. . SECTION 9: Physical and chemical properties Information on basic physical and chemical properties Appearance Odor pH Melting point / melting range Boiling point / boiling range Flash point Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure Relative density Specific gravity Solubility Partition coefficient: n-octanol/water Explosive properties Other information No data available. Reactivity Chemical stability Possibility of hazardous reactions Conditions to avoid Incompatible materials liquid No data available 3-5 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available No data available No data available Mixture has not been tested SECTION 10: Stability and reactivity None known. °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested Stable under normal conditions. Hazardous reaction has not been reported. No information available. No dangerous reaction known under conditions of normal use. __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 4 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio Hazardous decomposition products No data available. SECTION 11: Toxicological information Information on toxicological effects There is no evidence available indicating acute toxicity. Principal Routes of Exposure Irritation Corrosivity Sensitization STOT – Single Exposure STOT – Repeated Exposure Carcinogenicity Mutagenicity Reproductive toxicity Aspiration hazard Toxicity Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification SECTION 12: Ecological information The environmental impact of this product has not been fully investigated. Persistence and degradability No information available. Bioaccumulative potential No information available. Results of PBT and vPvB assessment This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available. SECTION 13: Disposal considerations Waste treatment methods The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations. SECTION 14: Transport information IATA / ADR / DOT-US / IMDG Not classified as dangerous in the meaning of transport regulations UN number Not Applicable __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 5 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio UN proper shipping name Transport hazard class(es) Packing group Environmental hazards Not Applicable Special precautions for user Not Applicable Not Applicable Not Applicable Not Applicable Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable. US Federal Regulations SARA 313 This product is not regulated by SARA. SECTION 15: Regulatory information Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61) This product does not contains HAPs. US State Regulations California Proposition 65 This product does not contain any Proposition 65 chemicals. WHMIS Hazard Class Non-controlled This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR. National Regulations – Brazil Not regulated SECTION 16: Other information Reason for revision Revision number 2 Revision date 23-Nov-2021 Use as laboratory reagent. Scientific research and development. References • ECHA: http://echa.europa.eu/ • TOXNET: http://toxnet.nlm.nih.gov/ __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 6 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio • eChemPortal: http://www.echemportal.org/ • LOLI database: https://www.chemadvisor.com/loli-database “The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE” End of Safety Data Sheet __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 7 / 7 Product code S55R1113 Product name Enzyme Reconstitution Solution www.seer.bio Safety Data Sheet SECTION 1: Identification of the substance/mixture and of the company/undertaking Identification of the substance or mixture Product code: S55R1114 Product name: Reduction Solution Company/undertaking identification Name: Seer, Inc. Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000 24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC: Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970 For Research Use Only. Not for use in diagnostic procedures. GHS – Classification Signal Word WARNING Hazard pictograms Health hazards SECTION 2: Hazards identification ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 1 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Skin corrosion/irritation Serious eye damage/eye irritation Physical hazards Not Hazardous Environmental hazards Not Hazardous Hazard Statements H319 – Causes serious eye irritation H315 – Causes skin irritation Precautionary Statements Prevention P280 – Wear protective gloves/protective clothing/eye protection/face protection P264 – Wash hands thoroughly after handling Response Category 2 Category 2 P302 + P352 – IF ON SKIN: Wash with plenty of soap and water P362 + P364 – Take off all contaminated clothing and wash it before reuse P332 + P313 – If skin irritation occurs: Get medical advice/attention P305 + P351 + P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing P337 + P313 – If eye irritation persists: Get medical advice/attention Storage Not Applicable Disposal Not Applicable Other hazards Not Applicable HMIS Health Flammability Reactivity tris-(2-carboxyethyl)phosphine, hydrochloride 51805-45-9 ( 10-20 ) 2 0 0 51805-45- – 9 10-20 SECTION 3: Composition/information on ingredients Component CAS-No EINECS- No Weight % ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio We recommend handling all chemicals with caution. SECTION 4: First aid measures Description of first aid measures Skin contact Eye contact Ingestion Inhalation Notes to Physician Most important symptoms and effects, both acute and delayed H319 – Causes serious eye irritation H315 – Causes skin irritation Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures Extinguishing media Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available. Special hazards arising from the substance or mixture Not known Advice for fire-fighters Wear self-contained breathing apparatus and protective suit SECTION 6: Accidental release measures Personal precautions, protective equipment and emergency procedures Ensure adequate ventilation Avoid contact with skin, eyes or clothing Use personal protection equipment See Section 8 for more detail Environmental precautions No special environmental precautions required. Methods and material for containment and cleaning up Soak up with inert absorbent material. Reference to other sections See section 8 for more information. ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 3 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use. Immediate medical attention is required. Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required. Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur. Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician. Treat symptomatically. SECTION 7: Handling and storage Precautions for safe handling Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator. Conditions for safe storage, including any incompatibilities Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations. Specific end use(s) Use as laboratory reagent. Scientific research and development. SECTION 8: Exposure controls/personal protection Control parameters Chemical Name tris-(2-carboxyethyl)phosp hine, hydrochloride tris-(2-carboxyethyl)phosphine, hydrochloride Engineering measures Exposure controls None None None None OSHA PEL OSHA PEL (Ceiling) ACGIH OEL (TWA) ACGIH OEL (STEL) Chemical Name Brazil – OEL – TWAs (LTs) Brazil – OEL – Ceilings Brazil – OEL – Skin Designations None Ensure adequate ventilation, especially in confined areas. None None Personal Protective Equipment Respiratory protection Hand protection Eye protection Skin and Body Protection Hygiene Measures In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards. Glove material:. Nitrile rubber. with thickness (mm). :5. Break through time. (hours). :1. Recommended glove type has not been tested for use with product. Information is based on professional Knowledge. Tight sealing safety goggles. Wear laboratory coat for body protection. Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls No special environmental precautions required. SECTION 9: Physical and chemical properties Information on basic physical and chemical properties Appearance liquid ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 4 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Odor Odor Threshold pH Melting point / melting range Boiling point / boiling range Flash point Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure Relative density Specific gravity Solubility Partition coefficient: n-octanol/water Viscosity Explosive properties Oxidizing properties Other information No data available. Reactivity Chemical stability Possibility of hazardous reactions Conditions to avoid Incompatible materials Hazardous decomposition products No data available Mixture has not been tested 6-8 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Soluble in water No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested SECTION 10: Stability and reactivity °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested None known. Stable under normal conditions. Hazardous reaction has not been reported. None known. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. SECTION 11: Toxicological information Information on toxicological effects ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Chemical Name LD50 (oral,rat/mouse) LD50 (dermal,rat/rabbit) LC50 (inhalation,rat/mouse) tris-(2-carboxyethyl)phosphine, hydrochloride Principal Routes of Exposure Irritation No data available Skin irritation Irritating to eyes Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification No data available No data available Corrosivity Sensitization STOT – Single Exposure STOT Exposure – Repeated Carcinogenicity Mutagenicity Reproductive toxicity Aspiration hazard Toxicity SECTION 12: Ecological information The environmental impact of this product has not been fully investigated. Chemical Name tris-(2- carboxyethyl)phosphi ne, hydrochloride Freshwater Algae Data No data available Water Flea Data No data available Freshwater Fish Species Data No data available Microtox Data No data available log Pow No data available Persistence and degradability No information available. Bioaccumulative potential No information available. Results of PBT and vPvB assessment This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available. Waste treatment methods SECTION 13: Disposal considerations The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations. SECTION 14: Transport information ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio IATA / ADR / DOT-US / IMDG Classified as dangerous in the meaning of transport regulations UN number UN proper shipping name Transport hazard class(es) Packing group Environmental hazards Not Applicable Special precautions for user Not Applicable 3261 Corrosive liquid, acidic, organic, n.o.s. (Propanoic acid, 3,3′,3”-phosphinidynetris-, hydrochloride) 8 III Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable. This product is subject to the de minimis exceptions for dangerous goods / hazardous materials in accordance with the following regulations: IATA 2.6.10, ADR 3.5.1.4, and U.S. DOT 49 CFR 173.4b. SECTION 15: Regulatory information tris-(2-carboxyethyl)phosphine, hydrochloride – 51805-45-9 ( 10-20 ) US Federal Regulations SARA 313 This product is not regulated by SARA. Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61) This product does not contains HAPs. US State Regulations California Proposition 65 This product does not contain any Proposition 65 chemicals. WHMIS Hazard Class E – Corrosive material This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR. ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Component US TSCA National Regulations – Brazil Chemical Name CAS-No Brazil – National Agency for Sanitary Surveillance (ANVISA) Brazil – National List of Carcinogen Agents to Humans (LINACH) tris-(2- carboxyethyl)phosphin e, hydrochloride Reason for revision Revision number Revision date Use as laboratory reagent. Scientific research and development. References • ECHA: http://echa.europa.eu/ • TOXNET: http://toxnet.nlm.nih.gov/ • eChemPortal: http://www.echemportal.org/ • LOLI database: https://www.chemadvisor.com/loli-database “The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE” End of Safety Data Sheet 51805-45-9 Not Listed Not Listed SECTION 16: Other information 2 23-Nov-2021 ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 8 / 8 Product code S55R1114 Product name Reduction Solution www.seer.bio Safety Data Sheet SECTION 1: Identification of the substance/mixture and of the company/undertaking Identification of the substance or mixture Product code: S55R1115 Product name: Alkylation Solution Company/undertaking identification Name: Seer, Inc. Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000 24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC: Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970 For Research Use Only. Not for use in diagnostic procedures GHS – Classification Signal Word WARNING Hazard pictograms Health hazards SECTION 2: Hazards identification __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 1 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio Skin sensitization Physical hazards Not Hazardous Environmental hazards Not Hazardous Hazard Statements H317 – May cause an allergic skin reaction Precautionary Statements Prevention P280 – Wear protective gloves/protective clothing/eye protection/face protection P261 – Avoid breathing dust/fume/gas/mist/vapors/spray P272 – Contaminated work clothing should not be allowed out of the workplace Response P302 + P352 – IF ON SKIN: Wash with plenty of soap and water P333 + P313 – If skin irritation or rash occurs: Get medical advice/attention P362 + P364 – Take off all contaminated clothing and wash it before reuse Subcategory 1A Storage Not Applicable Disposal Not Applicable Other hazards Not Applicable HMIS Health 2 Flammability 0 Reactivity 0 SECTION 3: Composition/information on ingredients Component CAS-No EINECS- No 2-Chloroacetamide 79- 07-2 ( 0.1-1.0 ) 79-07-2 201-174-2 0.1-1.0 Weight % We recommend handling all chemicals with caution. __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 2 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio SECTION 4: First aid measures Description of first aid measures Skin contact Eye contact Ingestion Inhalation Notes to Physician Most important symptoms and effects, both acute and delayed H317 – May cause an allergic skin reaction Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures Extinguishing media Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available. Special hazards arising from the substance or mixture Not known Advice for fire-fighters Wear self-contained breathing apparatus and protective suit SECTION 6: Accidental release measures Personal precautions, protective equipment and emergency procedures Ensure adequate ventilation Avoid contact with skin, eyes or clothing Use personal protection equipment See Section 8 for more detail Environmental precautions Avoid discharge into drains and waterways whenever possible. Methods and material for containment and cleaning up Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use. Immediate medical attention is required. Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required. Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur. Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician. Treat symptomatically. Soak up with inert absorbent material. Reference to other sections See section 8 for more information. Precautions for safe handling SECTION 7: Handling and storage __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 3 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator. Conditions for safe storage, including any incompatibilities Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations. Specific end use(s) Use as laboratory reagent. Scientific research and development. SECTION 8: Exposure controls/personal protection Control parameters Chemical Name 2-Chloroacetamide Chemical Name 2-Chloroacetamide Engineering measures Exposure controls None None None Ensure adequate ventilation, especially in confined areas. OSHA PEL OSHA PEL (Ceiling) ACGIH OEL (TWA) ACGIH OEL (STEL) None None Brazil – OEL – TWAs (LTs) Brazil – OEL – Ceilings Brazil – OEL – Skin Designations None None Personal Protective Equipment Respiratory protection Hand protection Eye protection Skin and Body Protection Hygiene Measures In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards. Glove material:. Nitrile rubber. with thickness (mm). :5. Break through time. (hours). :1. Recommended glove type has not been tested for use with product. Information is based on professional Knowledge. Tight sealing safety goggles. Wear laboratory coat for body protection. Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls Avoid discharge into drains and waterways whenever possible. SECTION 9: Physical and chemical properties Information on basic physical and chemical properties Appearance liquid Odor Mixture has not been tested __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 4 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio Odor Threshold Mixture has not been tested 5-7 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Mixture has not been tested No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested SECTION 10: Stability and reactivity None known. pH Melting point / melting range Boiling point / boiling range Flash point Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure Relative density Specific gravity Solubility Partition coefficient: n-octanol/water Viscosity Explosive properties Oxidizing properties Other information No data available. Reactivity Chemical stability Possibility of hazardous reactions Conditions to avoid Incompatible materials Hazardous decomposition products °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested Stable under normal conditions. Hazardous reaction has not been reported. None known. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. SECTION 11: Toxicological information Information on toxicological effects __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 5 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio LD50 (dermal,rat/rabbit) LC50 (inhalation,rat/mouse) Chemical Name LD50 (oral,rat/mouse) 2-Chloroacetamide Principal Routes of Exposure Irritation Corrosivity Sensitization STOT – Single Exposure STOT – Repeated Exposure Carcinogenicity Mutagenicity Reproductive toxicity Aspiration hazard Toxicity = 138 mg/kg (Rat) No data available Conclusive but not sufficient for classification Conclusive but not sufficient for classification May cause sensitization by skin contact Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification Conclusive but not sufficient for classification SECTION 12: Ecological information No data available The environmental impa ct of this product has not been fully investigated. Chemical Name Freshwater Algae Data 2-Chloroacetamide No data available Water Flea Data No data available Freshwater Fish Species Data No data available Microtox Data No data available log Pow No data available Persistence and degradability No information available. Bioaccumulative potential No information available. Results of PBT and vPvB assessment This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available. SECTION 13: Disposal considerations Waste treatment methods The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations. SECTION 14: Transport information __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 6 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio IATA / ADR / DOT-US / IMDG Not regulated in the meaning of transport regulations UN number UN proper shipping name Transport hazard class(es) Packing group Environmental hazards Not Applicable Special precautions for user Not Applicable Not Applicable Not Applicable Not Applicable Not Applicable Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable. __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 7 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio SECTION 15: Regulatory information Component US TSCA 2-Chloroacetamide 79- 07-2 ( 0.1-1.0 ) US Federal Regulations SARA 313 This product is not regulated by SARA. Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61) This product does not contains HAPs. US State Regulations California Proposition 65 This product does not contain any Proposition 65 chemicals. WHMIS Hazard Class D2B – Toxic materials Listed This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR. National Regulations – Brazil 2-Chloroacetamide Reason for revision Revision number Revision date 79-07-2 Not Listed SECTION 16: Other information 2 15-Nov-2021 Not Listed Chemical Name CAS-No Brazil – National Agency for Sanitary Surveillance (ANVISA) Brazil – National List of Carcinogen Agents to Humans (LINACH) Use as laboratory reagent. Scientific research and development. References • ECHA: http://echa.europa.eu/ __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 8 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio • TOXNET: http://toxnet.nlm.nih.gov/ • eChemPortal: http://www.echemportal.org/ • LOLI database: https://www.chemadvisor.com/loli-database “The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE” End of Safety Data Sheet __________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 9 / 9 Product code S55R1115 Product name Alkylation Solution www.seer.bio Safety Data Sheet SECTION 1: Identification of the substance/mixture and of the company/undertaking Identification of the substance or mixture Product code: S55R1116 Product name: Trypsin / LysC Protease MS Grade Company/undertaking identification Name: Seer, Inc. Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000 24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC: Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970 For Research Use Only. Not for use in diagnostic procedures. SECTION 2: Hazards identification GHS – Classification Signal Word DANGER Hazard pictograms Health hazards Respiratory sensitization __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 1 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio Category 1 Physical hazards Not Hazardous Environmental hazards Not Hazardous Hazard Statements H334 – May cause allergy or asthma symptoms or breathing difficulties if inhaled Precautionary Statements Prevention P280 – Wear protective gloves/protective clothing/eye protection/face protection P284 – In case of inadequate ventilation wear respiratory protection P271 – Use only outdoors or in a well-ventilated area P261 – Avoid breathing dust/fume/gas/mist/vapors/spray P264 – Wash hands thoroughly after handling Response P304 + P340 – IF INHALED: Remove person to fresh air and keep comfortable for breathing P342 + P311 – If experiencing respiratory symptoms: Call a POISON CENTER or doctor/physician Storage Not Applicable Disposal P501 – Dispose of contents/ container to an approved waste disposal plant Other hazards Not Applicable HMIS Health 2 Flammability 0 Reactivity 0 SECTION 3: Composition/information on ingredients Component CAS-No EINECS- No Trypsin 9002- 07-7 ( 3-5 ) 9002-07-7 232-650-8 3-5 Weight % We recommend handling all chemicals with caution. SECTION 4: First aid measures __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 2 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio Description of first aid measures Skin contact Eye contact Ingestion Inhalation Notes to Physician Most important symptoms and effects, both acute and delayed H334 – May cause allergy or asthma symptoms or breathing difficulties if inhaled Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures Extinguishing media Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available. Special hazards arising from the substance or mixture Not known Advice for fire-fighters Wear self-contained breathing apparatus and protective suit SECTION 6: Accidental release measures Personal precautions, protective equipment and emergency procedures Ensure adequate ventilation Avoid contact with skin, eyes or clothing Use personal protection equipment See Section 8 for more detail. Environmental precautions No special environmental precautions required. Methods and material for containment and cleaning up Take up mechanically, placing in appropriate containers for disposal. Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use. Immediate medical attention is required. Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required. Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur. Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician. Treat symptomatically. Reference to other sections See section 8 for more information. Precautions for safe handling SECTION 7: Handling and storage Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator. __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 3 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio Conditions for safe storage, including any incompatibilities Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations. Specific end use(s) Use as laboratory reagent. Scientific research and development. SECTION 8: Exposure controls/personal protection Control parameters Chemical Name Trypsin Chemical Name Trypsin Engineering measures Exposure controls None None None Ensure adequate ventilation, especially in confined areas. OSHA PEL OSHA PEL (Ceiling) ACGIH OEL (TWA) ACGIH OEL (STEL) None None Brazil – OEL – TWAs (LTs) Brazil – OEL – Ceilings Brazil – OEL – Skin Designations None None Personal Protective Equipment Respiratory protection Hand protection Eye protection Skin and Body Protection Hygiene Measures In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards. Glove material:. Nitrile rubber. with thickness (mm). :5. Break through time. (hours). :1. Recommended glove type has not been tested for use with product. Information is based on professional Knowledge. Tight sealing safety goggles. Wear laboratory coat for body protection. Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls No special environmental precautions required. SECTION 9: Physical and chemical properties Information on basic physical and chemical properties Appearance Odor Odor Threshold Solid Mixture has not been tested Mixture has not been tested __________________________________________________________________________________________________________________ _ Revision date 2021-11-23 Page 4 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio Melting point / melting range Boiling point / boiling range Flash point Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure Relative density Specific gravity Solubility Partition coefficient: n-octanol/water Viscosity Explosive properties Oxidizing properties Other information No data available. Reactivity Chemical stability Possibility of hazardous reactions Conditions to avoid Incompatible materials Hazardous decomposition products °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Mixture has not been tested No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested SECTION 10: Stability and reactivity None known. °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested Stable under normal conditions. Hazardous reaction has not been reported. No information available. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. SECTION 11: Toxicological information Information on toxicological effects LD50 (dermal,rat/rabbit) LC50 (inhalation,rat/mouse) Trypsin Chemical Name LD50 (oral,rat/mouse) > 5 g/kg (Rat) No data available No data available
__________________________________________________________________________________________________________________ _
Revision date 2021-11-23 Page 5 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio

Principal Routes of Exposure
Irritation Corrosivity
Sensitization
STOT – Single Exposure
STOT – Repeated Exposure
Carcinogenicity
Mutagenicity
Reproductive toxicity Aspiration hazard
Toxicity
Conclusive but not sufficient for classification Conclusive but not sufficient for classification
May cause sensitization by inhalation
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification Conclusive but not sufficient for classification
SECTION 12: Ecological information
The environmental impa
ct of this product has not been fully investigated.
Chemical Name Freshwater Algae Data
Trypsin No data available
Water Flea Data
No data available
Freshwater Fish Species Data No data available
Microtox Data
No data available
log Pow
No data available
Persistence and degradability No information available. Bioaccumulative potential No information available.
Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB.
Other adverse effects No information available.
SECTION 13: Disposal considerations
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations.
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not regulated in the meaning of transport regulations.
UN number Not Applicable __________________________________________________________________________________________________________________
_
Revision date 2021-11-23 Page 6 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade
www.seer.bio

UN proper shipping name Transport hazard class(es) Packing group
Environmental hazards
Not Applicable
Special precautions for user
Not Applicable
Not Applicable Not Applicable Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code
Not Applicable.
__________________________________________________________________________________________________________________ _
Revision date 2021-11-23 Page 7 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio

SECTION 15: Regulatory information
Component
US TSCA
Trypsin 9002- 07-7 ( 3-5 )
US Federal Regulations SARA 313
This product is not regulated by SARA.
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contains HAPs.
US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
D2A – Very toxic materials
Listed
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Trypsin
Reason for revision Revision number Revision date
9002-07-7 Not Listed Not Listed
SECTION 16: Other information
2 23-Nov-2021
Chemical Name
CAS-No
Brazil – National Agency for Sanitary Surveillance (ANVISA)
Brazil – National List of Carcinogen Agents to Humans (LINACH)
Use as laboratory reagent. Scientific research and development.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
__________________________________________________________________________________________________________________ _
Revision date 2021-11-23 Page 8 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio

• LOLI database: https://www.chemadvisor.com/loli-database
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
__________________________________________________________________________________________________________________ _
Revision date 2021-11-23 Page 9 / 9 Product code S55R1116 Product name Trypsin / LysC Protease MS Grade www.seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1121
Product name: Peptide Clean Up Plate
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
GHS Classification Signal Word
None
Hazard pictograms
None
Health hazards
Not classified
Physical hazards
Not classified
SECTION 2: Hazards identification
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 1 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Environmental hazards
Not classified
Hazard Statements
Not Applicable
Precautionary Statements Prevention
Not Applicable
Response
Not Applicable
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
Health Flammability Reactivity
Component
20-30 )
Description of first aid measures Skin contact
Eye contact
Ingestion Inhalation
0 0 0
SECTION 3: Composition/information on ingredients
CAS No.
Common name
EINECS-No
Weight-%
– –
The product contains no substances which at their given concentration, are considered to be hazardous to health.
DMSO 67-68-5 67-68-5 (
20-30
SECTION 4: First aid measures
Rinse skin with water. Immediate medical attention is not required.
Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice.
Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary.
Treat symptomatically.
Notes to Physician
Most important symptoms and effects, both acute and delayed Not Applicable
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Indication of any immediate medical attention and special treatment needed
None.
SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable
extinguishing media No information available. Special hazards arising from the substance or mixture
Not known
Protective equipment and precautions for firefighters
Standard procedure for chemical fires.
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Always wear recommended Personal Protective Equipment Use personal protection equipment
See section 8 for more information
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up
Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
Precautions for safe handling
SECTION 7: Handling and storage
Use personal protective equipment as required. No special handling advices are necessary.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers.
Specific end use(s)
Use as laboratory reagent. Scientific research and development.
Control parameters
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 3 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
SECTION 8: Exposure controls/personal protection
Chemical Name
OSHA PEL
OSHA PEL (Ceiling)
ACGIH OEL (TWA)
ACGIH OEL (STEL)
www.seer.bio

DMSO
None None None None
Chemical Name
Brazil – OEL – TWAs (LTs)
Brazil – OEL – Ceilings
Brazil – OEL – Skin Designations
DMSO Engineering Measures
None None None Ensure adequate ventilation, especially in confined areas.
Exposure controls
Personal Protective Equipment
Respiratory protection
Hand protection
Eye protection
Skin and Body Protection
Hygiene Measures
In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Wear suitable gloves. Glove material: Compatible chemical-resistant gloves. Tight sealing safety goggles.
Wear suitable protective clothing.
Handle in accordance with good industrial hygiene and safety practice
Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties
Appearance Odor
Odor Threshold
Molecular Weight
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate
Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Vapor density Relative density Specific gravity Solubility
liquid
No data available
No data
No data
°C No data °C No data °C No data °C No data °C No data No data
No data available No data
No data
No data
No data
No data
No data
No data available
°F No data °F No data °F No data °F No data °F No data
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 4 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Partition coefficient: n-octanol/water Viscosity
Explosive properties
Oxidizing properties
Other information
No data available.
Reactivity Chemical stability
Possibility of hazardous reactions
Conditions to avoid Incompatible materials
Hazardous decomposition products
No data available
No data No data No data
SECTION 10: Stability and reactivity
None known.
Stable under normal conditions. Hazardous reaction has not been reported.
No information available.
No dangerous reaction known under conditions of normal use. No data available.
SECTION 11: Toxicological information
Information on toxicological effects
Chemical Name
Oral LD50
Dermal LD50
Inhalation LC50
DMSO = 14500 mg/kg (Rat) = 28300 mg/kg No data available >5.33mg/L(Rat) (Rat)
Principal Routes of Exposure
Acute toxicity Data are conclusive but insufficient for classification.
Skin corrosion/irritation Data are conclusive but insufficient for classification
Serious eye damage/irritationData are conclusive but insufficient for classification
Respiratory or skin Data are conclusive but insufficient for classification sensitization
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – single exposure
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – repeated exposure
Carcinogenicity
Germ cell mutagenicity
Reproductive toxicity
Data are conclusive but insufficient for classification Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Aspiration hazard Data are conclusive but insufficient for classification
SECTION 12: Ecological information
Ecotoxicity
The environmental impact of this product has not been fully investigated.
Chemical Name DMSO
Mobility in soil
Toxicity to algae
Skeletonema costatum EC5012350
– 25500 mg/L (96 h)
Toxicity to daphnia and other aquatic invertebrates Daphnia species EC50=7000 mg/L (24 h)
Toxicity to fish
No data available
Microtox Data
No data available
log Pow
logPow-2.03
No information available.
Persistence and degradability No information available. Bioaccumulative
potential No information available.
Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available.
SECTION 13: Disposal considerations
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not classified as dangerous in the meaning of transport regulations
UN number
UN proper shipping name Transport hazard class(es) Packing group
Environmental hazards
Not Applicable
Special precautions for user
Not Applicable
Not Applicable Not Applicable Not Applicable Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code
Not Applicable.
SECTION 15: Regulatory information
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Component
US TSCA
DMSO Listed 67-68-5 ( 20-30 )
US Federal Regulations SARA 313
This product is not regulated by SARA.
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contain HAPs
US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
Non-controlled
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
DMSO 67-68-5 Not Listed Not Listed
Chemical Name
CAS No.
Brazil – National Agency for Sanitary Surveillance (ANVISA)
Brazil – National List of Carcinogen Agents to Humans (LINACH)
Reason for revision Revision number Revision date
SECTION 16: Other information
SDS sections updated. 2
23-Nov-2021
Use as laboratory reagent. Scientific research and development.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution.
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
__________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 8 / 8 Product code S55R1121 Product name Peptide Clean-up Plate
www.seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1131
Product name: Control Dilution Solution
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
GHS Classification Signal Word None Hazard pictograms None
Health hazards Not Hazardous Physical hazards Not Hazardous
SECTION 2: Hazards identification
Environmental hazards Not Hazardous
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 1 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

Hazard Statements
Not Applicable
Precautionary Statements Prevention
Not Applicable
Response
Not Applicable
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
The product contains no substances which at their given concentration, are considered to be hazardous to health. We recommend handling all chemicals with caution.
Health 0 Flammability 0 Reactivity 0
SECTION 3: Composition/information on ingredients
Skin contact Eye contact
Ingestion
Inhalation
Rinse skin with water. Immediate medical attention is not required.
Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice.
Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary.
Treat symptomatically.
SECTION 4: First aid measures
Description of first aid measures
Notes to Physician
Most important symptoms and effects, both acute and delayed Not Applicable
Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures
Extinguishing media
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 2 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available.
Special hazards arising from the substance or mixture Not known
Protective equipment and precautions for firefighters Standard procedure for chemical fires.
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Always wear recommended Personal Protective Equipment
Use personal protection equipment See section 8 for more information
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
SECTION 7: Handling and storage
Precautions for safe handling
Use personal protective equipment as required. No special handling advices are necessary.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers.
Specific end use(s)
For research use only.
SECTION 8: Exposure controls/personal protection
Control parameters
Exposure Limits Contains no substances with occupational exposure limit
values.
Engineering Measures Ensure adequate ventilation, especially in confined areas.
Exposure controls
Personal Protective Equipment
Respiratory protection In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Hand protection Wear suitable gloves. Glove material: Compatible chemical-resistant gloves. ___________________________________________________________________________________________________________________
Revision date 2021-11-15 Page 3 / 8 Product code S55R1131 Product name Control Dilution Solution www.seer.bio

Eye protection Tight sealing safety goggles. Skin and Body Protection Wear suitable protective clothing.
Hygiene Measures Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties
Appearance Color
Odor
Odor Threshold Molecular Weight pH
Melting point / melting range
Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Vapor density Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Viscosity
Explosive properties Oxidizing properties Other information No data.
Reactivity Chemical stability
liquid
clear, Colorless No data
No data
No data
6-8
°C No data
°C No data
°C No data
°C No data
°C No data
No data No data No data No data No data No data No data No data No data No data
No data No data No data
°F No data °F No data °F No data °F No data °F No data
SECTION 10: Stability and reactivity
None known.
Stable under normal conditions.
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 4 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

Possibility of hazardous reactions
Conditions to avoid
Incompatible materials
Hazardous decomposition products
Hazardous reaction has not been reported.
No information available.
No dangerous reaction known under conditions of normal use.
No data available.
SECTION 11: Toxicological information
Information on toxicological effects
There is no evidence available indicating acute toxicity.
Principal Routes of Exposure
Acute toxicity Data are conclusive but insufficient for classification.
Skin corrosion/irritation Data are conclusive but insufficient for classification Serious eye damage/irritationData are conclusive but insufficient for classification Respiratory or skin Data are conclusive but insufficient for classification sensitization
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – single exposure
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – repeated exposure
Carcinogenicity
Germ cell mutagenicity Reproductive toxicity
Aspiration hazard
Ecotoxicity
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
SECTION 12: Ecological information
Contains no substances known to be hazardous to the environment or not degradable in waste water treatment plants.
Mobility in soil No information available.
Persistence and degradability No information available. Bioaccumulative potential No
information available. ___________________________________________________________________________________________________________________
Revision date 2021-11-15 Page 5 / 8 Product code S55R1131 Product name Control Dilution Solution www.seer.bio

Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available.
SECTION 13: Disposal considerations
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not regulated in the meaning of transport regulations
UN number
UN proper shipping name Transport hazard class(es)
Packing group
Environmental hazards Not Applicable Special precautions for user
Not Applicable Not Applicable Not Applicable Not Applicable
Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable.
SECTION 15: Regulatory information
US Federal Regulations SARA 313
This product is not regulated by SARA.
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contain HAPs
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 6 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
Non-controlled
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Not regulated
SECTION 16: Other information
Reason for revision
Revision number 2
Revision date 15-Nov-2021
For research use only. Not for use in diagnostic procedures.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
Abbreviations and acronyms
TWA – Time-Weighted Average
OELs – Occupational Exposure Limits
STEL – Short Term Exposure Limit
DSL/NDSL – Canadian Domestic Substances List/Non-Domestic Substances List
KECL – Korean Existing and Evaluated Chemical Substances
ENCS – Japan Existing and New Chemical Substances
IECSC – China Inventory of Existing Chemical Substances
PICCS – Philippines Inventory of Chemicals and Chemical Substances
AICS – Australian Inventory of Chemical Substances
NZIoC – New Zealand Inventory of Chemicals
EINECS/ELINCS – European Inventory of Existing Chemical Substances/European List of Notified Chemical Substances TSCA – United States Toxic Substances Control Act Section 8(b) Inventory CEPA – Canadian Environmental Protection Act
EPA – Environmental Protection Agency
OSHA – Occupational Safety and Health Administration of the US Department of Labor
IATA – International Air Transport Association DOT – Department of Transportation
IMDG – International Maritime Dangerous Goods
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 7 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

ACGIH – American Conference of Governmental Industrial Hygienists NIOSH – National Institute for Occupational Safety and Health
AIHA – American Industrial Hygiene Association
HMIS – Department of Defense Hazardous Materials Information System NTP – National Toxicology Program
IARC – International Agency for Research on Cancer
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein.
THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
___________________________________________________________________________________________________________________ Revision date 2021-11-15 Page 8 / 8 Product code S55R1131 Product name Control Dilution Solution
www.seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1132 Product name: Wash Solution C
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887 Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
GHS Classification Signal Word None Hazard pictograms None
Health hazards Not Hazardous Physical hazards Not Hazardous
SECTION 2: Hazards identification
Environmental hazards Not Hazardous
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 1 / 8 Product code S55R1132 Product name Wash Solution C
www.seer.bio

Hazard Statements
Not Applicable
Precautionary Statements Prevention
Not Applicable
Response
Not Applicable
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
The product contains no substances which at their given concentration, are considered to be hazardous to health. We recommend handling all chemicals with caution.
Health 0 Flammability 0 Reactivity 0
SECTION 3: Composition/information on ingredients
Skin contact Eye contact
Ingestion
Inhalation
Rinse skin with water. Immediate medical attention is not required.
Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice.
Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary.
Treat symptomatically.
SECTION 4: First aid measures
Description of first aid measures
Notes to Physician
Most important symptoms and effects, both acute and delayed Not Applicable
Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures
Extinguishing media
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 8 Product code S55R1132 Product name Wash Solution C
www.seer.bio

Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable extinguishing media No information available.
Special hazards arising from the substance or mixture Not known
Protective equipment and precautions for firefighters Standard procedure for chemical fires.
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Always wear recommended Personal Protective Equipment
Use personal protection equipment See section 8 for more information
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
SECTION 7: Handling and storage
Precautions for safe handling
Use personal protective equipment as required. No special handling advices are necessary.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers.
Specific end use(s)
For research use only.
SECTION 8: Exposure controls/personal protection
Control parameters
Exposure Limits Contains no substances with occupational exposure limit
values.
Engineering Measures Ensure adequate ventilation, especially in confined areas.
Exposure controls
Personal Protective Equipment
Respiratory protection In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
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Hand protection Wear suitable gloves. Glove material: Compatible chemical-resistant gloves.
Eye protection Tight sealing safety goggles. Skin and Body Protection Wear suitable protective clothing.
Hygiene Measures Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties
Appearance Color
Odor
Odor Threshold Molecular Weight pH
Melting point / melting range
Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Vapor density Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Viscosity
Explosive properties Oxidizing properties Other information No data.
Reactivity Chemical stability
liquid
clear, Colorless No data
No data
No data
6-8
°C No data
°C No data
°C No data
°C No data
°C No data
No data No data No data No data No data No data No data No data No data No data
No data No data No data
°F No data °F No data °F No data °F No data °F No data
SECTION 10: Stability and reactivity
None known.
Stable under normal conditions.
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www.seer.bio

Possibility of hazardous reactions
Conditions to avoid
Incompatible materials
Hazardous decomposition products
Hazardous reaction has not been reported.
No information available.
No dangerous reaction known under conditions of normal use.
No data available.
SECTION 11: Toxicological information
Information on toxicological effects
There is no evidence available indicating acute toxicity.
Principal Routes of Exposure
Acute toxicity Data are conclusive but insufficient for classification.
Skin corrosion/irritation Data are conclusive but insufficient for classification
Serious eye damage/irritationData are conclusive but insufficient for classification
Respiratory or skin Data are conclusive but insufficient for classification sensitization
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – single exposure
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – repeated exposure
Carcinogenicity
Germ cell mutagenicity Reproductive toxicity
Aspiration hazard
Ecotoxicity
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification
SECTION 12: Ecological information
Contains no substances known to be hazardous to the environment or not degradable in waste water treatment plants.
Mobility in soil No information available.
Persistence and degradability No information available. Bioaccumulative potential No
information available.
Results of PBT and vPvB assessment
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www.seer.bio

This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available.
SECTION 13: Disposal considerations
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not regulated in the meaning of transport regulations
UN number
UN proper shipping name Transport hazard class(es)
Packing group
Environmental hazards Not Applicable Special precautions for user
Not Applicable Not Applicable Not Applicable Not Applicable
Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable.
SECTION 15: Regulatory information
US Federal Regulations SARA 313
This product is not regulated by SARA.
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contain HAPs
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 8 Product code S55R1132 Product name Wash Solution C
www.seer.bio

US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
Non-controlled
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Not regulated
SECTION 16: Other information
Reason for revision
Revision number 2
Revision date 23-Nov-2021
For research use only. Not for use in diagnostic procedures.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
Abbreviations and acronyms
TWA – Time-Weighted Average
OELs – Occupational Exposure Limits
STEL – Short Term Exposure Limit
DSL/NDSL – Canadian Domestic Substances List/Non-Domestic Substances List
KECL – Korean Existing and Evaluated Chemical Substances
ENCS – Japan Existing and New Chemical Substances
IECSC – China Inventory of Existing Chemical Substances
PICCS – Philippines Inventory of Chemicals and Chemical Substances
AICS – Australian Inventory of Chemical Substances
NZIoC – New Zealand Inventory of Chemicals
EINECS/ELINCS – European Inventory of Existing Chemical Substances/European List of Notified Chemical Substances TSCA – United States Toxic Substances Control Act Section 8(b) Inventory CEPA – Canadian Environmental Protection Act
EPA – Environmental Protection Agency
OSHA – Occupational Safety and Health Administration of the US Department of Labor
IATA – International Air Transport Association DOT – Department of Transportation
IMDG – International Maritime Dangerous Goods
ACGIH – American Conference of Governmental Industrial Hygienists
NIOSH – National Institute for Occupational Safety and Health
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AIHA – American Industrial Hygiene Association
HMIS – Department of Defense Hazardous Materials Information System NTP – National Toxicology Program
IARC – International Agency for Research on Cancer
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein.
THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
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Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1133
Product name: Peptide Wash Solution A
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
GHS Classification Signal Word
None
Hazard pictograms
None
Health hazards
Not classified
Physical hazards
Not classified
SECTION 2: Hazards identification
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www.seer.bio

Environmental hazards
Not classified
Hazard Statements
Not Applicable
Precautionary Statements Prevention
Not Applicable
Response
Not Applicable
Storage
Not Applicable
Disposal
Not Applicable
Other hazards
Not Applicable
HMIS
Health 0 Flammability 0 Reactivity 0
SECTION 3: Composition/information on ingredients
The product contains no substances which at their given concentration, are considered to be hazardous to health.
Description of first aid measures Skin contact
Eye contact
Ingestion Inhalation
SECTION 4: First aid measures
Rinse skin with water. Immediate medical attention is not required.
Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.
Not expected to present a significant ingestion hazard under anticipated conditions of normal use. If you feel unwell, seek medical advice.
Not expected to be an inhalation hazard under anticipated conditions of normal use of this material. Consult a physician if necessary.
Treat symptomatically.
Notes to Physician
Most important symptoms and effects, both acute and delayed Not Applicable
Indication of any immediate medical attention and special treatment needed
None.
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www.thermofisher.com

SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable
extinguishing media No information available. Special hazards arising from the substance or mixture
Not known
Protective equipment and precautions for firefighters
Standard procedure for chemical fires.
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Always wear recommended Personal Protective Equipment Use personal protection equipment
See section 8 for more information
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up
Take up mechanically, placing in appropriate containers for disposal.
Reference to other sections
See section 8 for more information.
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www.seer.bio

SECTION 7: Handling and storage
Precautions for safe handling
Use personal protective equipment as required. No special handling advices are necessary.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers.
Specific end use(s)
Use as laboratory reagent. Scientific research and development.
SECTION 8: Exposure controls/personal protection
Control parameters
Exposure Limits Contains no substances with occupational exposure limit values.
Engineering Measures Ensure adequate ventilation, especially in confined areas. Exposure controls
Personal Protective Equipment
Respiratory protection
Hand protection
Eye protection
Skin and Body Protection
Hygiene Measures
In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Wear suitable gloves. Glove material: Compatible chemical-resistant gloves. Tight sealing safety goggles.
Wear suitable protective clothing.
Handle in accordance with good industrial hygiene and safety practice
Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties Appearance liquid
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www.seer.bio

Color
Odor
Odor Threshold
Molecular Weight
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate
Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Vapor density Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Viscosity
Explosive properties
Oxidizing properties
Other information
No data available.
Reactivity Chemical stability
Possibility of hazardous reactions
clear pungent No data No data
°C No data °C No data °C No data °C No data °C No data No data
No data available No data
No data
No data
No data
No data
No data
No data available No data available
No data No data No data
SECTION 10: Stability and reactivity
None known.
°F No data °F No data °F No data °F No data °F No data
Stable under normal conditions. Hazardous reaction has not been reported.
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www.seer.bio

Conditions to avoid Incompatible materials
Hazardous decomposition products
No information available.
No dangerous reaction known under conditions of normal use. No data available.
SECTION 11: Toxicological information
Information on toxicological effects
There is no evidence available indicating acute toxicity.
Principal Routes of Exposure
Acute toxicity Data are conclusive but insufficient for classification. Skin corrosion/irritation Data are conclusive but insufficient for classification Serious eye damage/irritationData are conclusive but insufficient for classification Respiratory or skin Data are conclusive but insufficient for classification sensitization
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – single exposure
Specific target organ toxicity Data are conclusive but insufficient for classification (STOT) – repeated exposure
Carcinogenicity
Germ cell mutagenicity Reproductive toxicity Aspiration hazard
Ecotoxicity
Data are conclusive but insufficient for classification Data are conclusive but insufficient for classification
Data are conclusive but insufficient for classification Data are conclusive but insufficient for classification
SECTION 12: Ecological information
The environmental impact of this product has not been fully investigated.
Mobility in soil No information available.
Persistence and degradability No information available. Bioaccumulative potential No information available.
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www.seer.bio

Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB. Other adverse effects No information available.
_________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 9 Product code S55R1133 Product name Peptide Wash Solution A
www.seer.bio

Waste treatment methods
Not Applicable.
US Federal Regulations SARA 313
This product is not regulated by SARA.
SECTION 15: Regulatory information
SECTION 13: Disposal considerations
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Not classified as dangerous in the meaning of transport regulations
UN number
UN proper shipping name Transport hazard class(es) Packing group
Environmental hazards
Not Applicable
Special precautions for user
Not Applicable
Not Applicable Not Applicable Not Applicable Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
This product does not contain HAPs
US State Regulations California Proposition 65
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
Non-controlled
__________________________________________________________________________________________________________________ _
Revision date 2021-11-23 Page 8 / 9 Product code S55R1133 Product name Peptide Wash Solution A www.seer.bio

This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Not regulated
Reason for revision
Revision number
Revision date
Use as laboratory reagent. Scientific research and development.
References
SECTION 16: Other information
SDS sections updated. 2
23-Nov-2021
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein.
THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
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www.seer.bio

Safety Data Sheet
SECTION 1: Identification of the substance/mixture and of the company/undertaking
Identification of the substance or mixture
Product code: S55R1134
Product name: Peptide Wash Solution B
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
GHS – Classification Signal Word DANGER Hazard pictograms
Health hazards
Acute dermal toxicity
Category 4
SECTION 2: Hazards identification
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Serious eye damage/eye irritation
Physical hazards
GHS Physical Hazard
GHS Physical Hazard Category Number
Environmental hazards
Not classified
Hazard Statements
H225 – Highly flammable liquid and vapor H312 – Harmful in contact with skin
H319 – Causes serious eye irritation
Precautionary Statements
Prevention
Category 2
Flammable liquids Category 2
P280 – Wear protective gloves/protective clothing/eye protection/face protection
P210 – Keep away from heat, hot surfaces, sparks, open flames and other ignition sources. No smoking P241 – Use explosion-proof electrical/ ventilating/ lighting/ equipment
P242 – Use non-sparking tools
P243 – Take action to prevent static discharges
P233 – Keep container tightly closed
P264 – Wash hands thoroughly after handling
Response
P303 + P361 + P353 – IF ON SKIN (or hair): Remove/Take off immediately all contaminated clothing. Rinse skin with water/shower
P302 + P352 – IF ON SKIN: Wash with plenty of soap and water
P312 – Call a POISON CENTER or doctor/physician if you feel unwell
P305 + P351 + P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing
P337 + P313 – If eye irritation persists: Get medical advice/attention
Storage
P403 + P235 – Store in a well-ventilated place. Keep cool
Disposal
P501 – Dispose of contents/ container to an approved waste disposal plant
Other hazards
Not Applicable
HMIS
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 2 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio
Health 2 Flammability 3 Reactivity 0

SECTION 3: Composition/information on ingredients
Component
CAS- No
EINECS- No
Acetonitrile 75- 75-05-8 200-835- 50-75 05-8 ( 50-75 ) 2
We recommend handling all chemicals with caution.
Description of first aid measures
Weight %
SECTION 4: First aid measures
Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use.
Immediate medical attention is required.
Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required.
Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur. Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician.
Notes to Physician
Most important symptoms and effects, both acute and delayed
H225 – Highly flammable liquid and vapor H312 – Harmful in contact with skin H319 – Causes serious eye irritation
Indication of any immediate medical attention and special treatment needed None. SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical.
Unsuitable extinguishing media No information available. Special hazards arising from the substance or mixture Not known
Advice for fire-fighters
Wear self-contained breathing apparatus and protective suit
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
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Skin contact
Eye contact Ingestion Inhalation
Treat symptomatically.

Avoid contact with skin, eyes or clothing
Use personal protection equipment See Section 8 for more detail
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up Soak up with inert absorbent material.
Reference to other sections
See section 8 for more information.
Precautions for safe handling
SECTION 7: Handling and storage
Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations.
Specific end use(s)
Use as laboratory reagent. Scientific research and development.
SECTION 8: Exposure controls/personal protection
Control parameters
Acetonitrile
Acetonitrile
40 ppm None 70 mg/m3 5 mg/m3
30 ppm 55 mg/m3
20 ppm None
None None
Chemical Name
OSHA PEL
OSHA PEL (Ceiling)
ACGIH OEL (TWA)
ACGIH OEL (STEL)
Brazil – OEL – TWAs (LTs)
Brazil – OEL – Ceilings
Brazil – OEL – Skin Designations
Chemical Name
Engineering measures Ensure adequate ventilation, especially in confined areas. Exposure controls
Personal Protective Equipment
Respiratory protection In case of insufficient ventilation wear respirators and components
tested and approved under appropriate government standards.
Hand protection Glove material:. Nitrile rubber. with thickness (mm). :5. Break through
time. (hours). :1.
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 4 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio

Recommended glove type has not been tested for use with product. Information is based on professional Knowledge.
Eye protection Tight sealing safety goggles.
Skin and Body Protection Wear laboratory coat for body protection.
Hygiene Measures Handle in accordance with good industrial hygiene and safety practice Environmental exposure controls
No special environmental precautions required.
SECTION 9: Physical and chemical properties
Information on basic physical and chemical properties
Appearance Odor
Odor Threshold pH
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature
liquid
Mixture has not been tested Mixture has not been tested
<3 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested Evaporation rate Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure Relative density Specific gravity Solubility Partition coefficient: n-octanol/water Viscosity Explosive properties Oxidizing properties Other information No data available. No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Mixture has not been tested No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested Reactivity Chemical stability Possibility of hazardous reactions SECTION 10: Stability and reactivity None known. Stable under normal conditions. Hazardous reaction has not been reported. ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio Conditions to avoid Incompatible materials Hazardous decomposition products Proximity to sources of ignition. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. SECTION 11: Toxicological information Information on toxicological effects Principal Routes of Exposure Chemical Name LD50 (oral,rat/mouse) LD50 (dermal,rat/rabbit) LC50 (inhalation,rat/mouse) Acetonitrile = 160 mg/kg (Rat) = 2460 mg/kg (Rat) >2000 μL/kg (Rabbit)
8 h 7551 ppm (Rat)
Irritation Corrosivity
Sensitization
STOT – Single Exposure
STOT – Repeated Exposure
Carcinogenicity
Mutagenicity
Irritating to eyes
Conclusive but not sufficient for classification Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification Conclusive but not sufficient for classification
Reproductive toxicityConclusive but not sufficient for classification
Aspiration hazard
Toxicity
Conclusive but not sufficient for classification
SECTION 12: Ecological information
The environmental impact of this product has not been fully investigated.
Chemical Name
Freshwate r Algae Data
Water Flea Data
Freshwater Fish Species Data
Microtox Data
log Pow
Acetonitrile
No data available
Daphnia pulex EC50=583
8 mg/L (18 h)
No data available
No data available
logPow- 0.34
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 6 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio

Persistence and degradability No information available. Bioaccumulative potential No information available.
Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB.
Other adverse effects No information available.
Waste treatment methods
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations.
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Classified as dangerous in the meaning of transport regulations UN number 1648
UN proper shipping name Acetonitrile
mixture Transport hazard class(es) 3 Packing group II
Environmental hazards Not Applicable Special precautions for user
Not Applicable
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code Not Applicable.
SECTION 15: Regulatory information
Acetonitrile 75-05-8 ( 50-75 ) Listed
US Federal Regulations
SARA 313
This product contains the following toxic chemical(s) subject to the notification requirements of section 313 of Title III of the Superfund Amendments and Reauthorization Act of 1986. This law requires certain manufacturers to report on annual emissions of specified chemicals and chemical categories. Please note that if you repackage, or otherwise redistribute, this product to industrial customers, a notice similar to this one should be sent to those customers.
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 7 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio
SECTION 13: Disposal considerations
Component
US TSCA

Chemical Name CAS-No Weight %
Acetonitrile 75-05-8 50-75
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
SARA 313 – Threshold Values
1.0
HAPS data
Present Present (XCN where X=H or any other group where a formal dissociation may occur. For example KCN or Ca[CN]2)
This product contains the following HAPs
Component
Acetonitrile 75-05-8 ( 50-75 )
US State Regulations California Proposition 65
CAS-No
75-05-8
Weight %
50-75
This product does not contain any Proposition 65 chemicals.
WHMIS Hazard Class
D2B – Toxic materials B2 – Flammable liquid
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Acetonitrile
Reason for revision Revision number Revision date
75-05-8 Not Listed
SECTION 16: Other information
Not Listed
Chemical Name
CAS-No
Brazil – National Agency for Sanitary Surveillance (ANVISA)
Brazil – National List of Carcinogen Agents to Humans (LINACH)
23-Nov-2021
Use as laboratory reagent. Scientific research and development.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
2
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“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein.
THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 9 / 9 Product code S55R1134 Product name Peptide Wash Solution B www.seer.bio

Safety Data Sheet
Product code: S55R1135
Product name: Peptide Elution Solution
Company/undertaking identification
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
24 hour Emergency Response for Hazardous Materials [or Dangerous Goods] Incident, Spill, Leak, Fire, Exposure, or Accident. Call CHEMTREC:
Within the USA + Canada: 1-800-424-9300 and 1-703-527-3887
Outside the USA + Canada: 1-703-741-5970
For Research Use Only. Not for use in diagnostic procedures.
SECTION 1: Identification of the substance/mixture and of the company/undertaking Identification of the substance or mixture
SECTION 2: Hazards identification
GHS – Classification Signal Word
DANGER
Hazard pictograms
Health hazards
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Acute dermal toxicity
Serious eye damage/eye irritation
Physical hazards
GHS Physical Hazard
GHS Physical Hazard Category Number
Environmental hazards
Not classified
Hazard Statements
H225 – Highly flammable liquid and vapor H312 – Harmful in contact with skin
H319 – Causes serious eye irritation
Precautionary Statements
Prevention
Category 4 Category 2
Flammable liquids Category 2
P280 – Wear protective gloves/protective clothing/eye protection/face protection
P210 – Keep away from heat, hot surfaces, sparks, open flames and other ignition sources. No smoking P241 – Use explosion-proof electrical/ ventilating/ lighting/ equipment
P242 – Use non-sparking tools
P243 – Take action to prevent static discharges
P233 – Keep container tightly closed
P264 – Wash hands thoroughly after handling
Response
P303 + P361 + P353 – IF ON SKIN (or hair): Remove/Take off immediately all contaminated clothing. Rinse skin with water/shower
P302 + P352 – IF ON SKIN: Wash with plenty of soap and water
P312 – Call a POISON CENTER or doctor/physician if you feel unwell
P305 + P351 + P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing
P337 + P313 – If eye irritation persists: Get medical advice/attention
Storage
P403 + P235 – Store in a well-ventilated place. Keep cool
Disposal
P501 – Dispose of contents/ container to an approved waste disposal plant
Other hazards
Not Applicable
HMIS
Health 2 Flammability 3 Reactivity 0
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SECTION 3: Composition/information on ingredients

Component
CAS-No
EINECS- No
Acetonitrile 75- 75-05-8 200-835-2 50-75 05-8 ( 50-75 )
We recommend handling all chemicals with caution.
Weight %
SECTION 4: First aid measures
Description of first aid measures Skin contact
Eye contact Ingestion Inhalation
Notes to Physician
Most important symptoms and effects, both acute and delayed
H225 – Highly flammable liquid and vapor H312 – Harmful in contact with skin H319 – Causes serious eye irritation
Indication of any immediate medical attention and special treatment needed
None.
SECTION 5: Firefighting measures
Extinguishing media
Suitable extinguishing media Water spray. Carbon dioxide (CO2). Foam. Dry chemical. Unsuitable
extinguishing media No information available. Special hazards arising from the substance or mixture
Not known
Advice for fire-fighters
Wear self-contained breathing apparatus and protective suit
SECTION 6: Accidental release measures
Personal precautions, protective equipment and emergency procedures
Ensure adequate ventilation
Avoid contact with skin, eyes or clothing Use personal protection equipment
See Section 8 for more detail
Environmental precautions
No special environmental precautions required.
Methods and material for containment and cleaning up
Soak up with inert absorbent material.
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Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing and gloves, including the inside, before re-use. Immediate medical attention is required.
Rinse immediately with plenty of water, also under the eyelids, for at least 15 minutes. Immediate medical attention is required.
Never give anything by mouth to an unconscious person. Do not induce vomiting without medical advice. Get medical attention if symptoms occur.
Remove to fresh air. If not breathing, give artificial respiration. If symptoms persist, call a physician.
Treat symptomatically.

Reference to other sections
See section 8 for more information.
Precautions for safe handling
SECTION 7: Handling and storage
Always wear recommended Personal Protective Equipment. See Section 8 for more detail. Do not get in eyes, on skin, or on clothing. Do not ingest. If during normal use the material presents a respiratory hazard, use only with adequate ventilation or wear appropriate respirator.
Conditions for safe storage, including any incompatibilities
Keep in a dry, cool and well-ventilated place. Keep in properly labeled containers. Store in accordance with local regulations.
Specific end use(s)
Use as laboratory reagent. Scientific research and development.
Control parameters
Acetonitrile
Chemical Name
Acetonitrile Engineering measures
20 ppm None
None None Ensure adequate ventilation, especially in confined areas.
SECTION 8: Exposure controls/personal protection
Chemical Name
OSHA PEL
OSHA PEL (Ceiling)
ACGIH OEL (TWA)
ACGIH OEL (STEL)
40 ppm None 70 mg/m3 5 mg/m3
Brazil – OEL – TWAs (LTs)
Brazil – OEL – Ceilings
Brazil – OEL – Skin Designations
30 ppm 55 mg/m3
Exposure controls
Personal Protective Equipment
Respiratory protection Hand protection
Eye protection
Skin and Body Protection
Hygiene Measures
In case of insufficient ventilation wear respirators and components tested and approved under appropriate government standards.
Glove material:. Nitrile rubber. with thickness (mm). :5. Break through time. (hours). :1.
Recommended glove type has not been tested for use with product. Information is based on professional Knowledge.
Tight sealing safety goggles.
Wear laboratory coat for body protection.
Handle in accordance with good industrial hygiene and safety practice
Environmental exposure controls
No special environmental precautions required.
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Information on basic physical and chemical properties
Appearance Odor
Odor Threshold pH
Melting point / melting range Boiling point / boiling range Flash point
Autoignition Temperature Decomposition temperature Evaporation rate
Flammability (solid, gas) Upper explosion limit Lower explosion limit Vapor Pressure
Relative density Specific gravity Solubility
Partition coefficient: n-octanol/water Viscosity
Explosive properties
Oxidizing properties
Other information
No data available.
Reactivity Chemical stability
Possibility of hazardous reactions
Conditions to avoid Incompatible materials
Hazardous decomposition products
liquid
Mixture has not been tested
Mixture has not been tested
<3 °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested °C Mixture has not been tested No data available Not Applicable Mixture has not been tested Mixture has not been tested Mixture has not been tested Mixture has not been tested No data available Mixture has not been tested No data available Mixture has not been tested Mixture has not been tested Mixture has not been tested SECTION 10: Stability and reactivity °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested °F Mixture has not been tested SECTION 9: Physical and chemical properties None known. Stable under normal conditions. Hazardous reaction has not been reported. Proximity to sources of ignition. No dangerous reaction known under conditions of normal use. No known hazardous decomposition products. ___________________________________________________________________________________________________________________ Revision date 2021-11-23 Page 5 / 8 Product code S55R1135 Product name Peptide Elution Solution www.seer.bio SECTION 11: Toxicological information Information on toxicological effects Acetonitrile = 160 mg/kg (Rat) = 2460 mg/kg (Rat) Principal Routes of Exposure >2000 μL/kg (Rabbit)
8 h 7551 ppm (Rat)
Chemical Name
LD50 (oral,rat/mouse)
LD50 (dermal,rat/rabbit)
LC50 (inhalation,rat/mouse)
Irritation
Corrosivity
Sensitization
STOT – Single Exposure
STOT – Repeated Exposure
Carcinogenicity Mutagenicity Reproductive toxicity
Aspiration hazard
Irritating to eyes
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
Conclusive but not sufficient for classification
SECTION 12: Ecological information
Toxicity
The environmental impact of this product has not been fully investigated.
Chemical Name Freshwater Water Flea Freshwater Algae Data Data Fish Species
Data
Persistence and degradability No information available. Bioaccumulative potential No information available.
Results of PBT and vPvB assessment
This mixture does not contain any substances that are assessed to be a PBT or a vPvB.
Other adverse effects No information available.
Waste treatment methods
Microtox Data
log Pow
No data available
logPow- 0.34
Acetonitrile
No data available
Daphnia pulex EC50=5838 mg/L (18
h)
No data available
SECTION 13: Disposal considerations
The generation of waste should be avoided or minimized wherever possible. Empty containers or liners may retain some product residues. This material and its container must be disposed of in according to approved disposal
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technique. Disposal of this product, its solutions or of any by-products, shall comply with the requirements of all applicable local, regional or national/federal regulations.
SECTION 14: Transport information
IATA / ADR / DOT-US / IMDG
Classified as dangerous in the meaning of transport regulations
UN number
UN proper shipping name Transport hazard class(es) Packing group
Environmental hazards
Not Applicable
Special precautions for user
Not Applicable
1648
Acetonitrile mixture 3
II
Transport in bulk according to Annex II of MARPOL 73/78 and the IBC Code
Not Applicable.
SECTION 15: Regulatory information
Component
US TSCA
Acetonitrile 75- 05-8 ( 50-75 )
Listed
US Federal Regulations
SARA 313
This product contains the following toxic chemical(s) subject to the notification requirements of section 313 of Title III of the Superfund Amendments and Reauthorization Act of 1986. This law requires certain manufacturers to report on annual emissions of specified chemicals and chemical categories. Please note that if you repackage, or otherwise redistribute, this product to industrial customers, a notice similar to this one should be sent to those customers.
Chemical Name CAS-No Weight %
Acetonitrile 75-05-8 50-75
Clean Air Act, Section 112 Hazardous Air Pollutants (HAPs) (see 40 CFR 61)
SARA 313 – Threshold Values
1.0
HAPS data
Present Present (XCN where X=H or any other group where a formal dissociation may occur. For example KCN or Ca[CN]2)
This product contains the following HAPs
Component
Acetonitrile 75-05-8 ( 50-75 )
US State Regulations California Proposition 65
CAS-No
75-05-8
Weight %
50-75
This product does not contain any Proposition 65 chemicals.
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WHMIS Hazard Class
D2B – Toxic materials B2 – Flammable liquid
This product has been classified in accordance with the hazard criteria of the Controlled Products Regulations (CPR) and the SDS contains all the information required by the CPR.
National Regulations – Brazil
Acetonitrile
Reason for revision Revision number Revision date
75-05-8 Not Listed
SECTION 16: Other information
Not Listed
Chemical Name
CAS-No
Brazil – National Agency for Sanitary Surveillance (ANVISA)
Brazil – National List of Carcinogen Agents to Humans (LINACH)
23-Nov-2021
Use as laboratory reagent. Scientific research and development.
References
• ECHA: http://echa.europa.eu/
• TOXNET: http://toxnet.nlm.nih.gov/
• eChemPortal: http://www.echemportal.org/
• LOLI database: https://www.chemadvisor.com/loli-database
2
“The above information was acquired by diligent search and/or investigation and the recommendations are based on prudent application of professional judgment. The information shall not be taken as being all inclusive and is to be used only as a guide. All materials and mixtures may present unknown hazards and should be used with caution. Since the Company cannot control the actual methods, volumes, or conditions of use, the Company shall not be held liable for any damages or losses resulting from the handling or from contact with the product as described herein. THE INFORMATION IN THIS SDS DOES NOT CONSTITUTE A WARRANTY, EXPRESSED OR IMPLIED,INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE”
End of Safety Data Sheet
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SECTION 1: IDENTIFICATION
1.1 Product Identifier:
Product Number and Name: S55R1140, Proteograph Nanoparticle Panel Index Number: Not Applicable
Registration Number: Not Applicable
CAS Number: Not Applicable
Safety Data Sheet
1.2 Recommended Use of the Chemical and Restrictions on Use: Laboratory chemicals, manufacture of substances
1.3 Supplier’s Details:
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
1.4 Emergency Phone Number: 650-453-0000 (M-F 9-5 PM PT)
SECTION 2: HAZARDS IDENTIFICATION
2.1 Classification of the Substance or Mixture:
GHS Classification in Accordance to 29 CFR 1910.1200: Not a hazardous substance or mixture 2.2 Label Element, Including Precautionary Statements:
Labeling GHS Labeling in accordance to 29 CFR 1910.1200: Pictogram(s): None
Signal Word: None
Hazard Statement(s): None
Precautionary Statement(s): None
2.3 Other Hazards which do not result in Classification: None SECTION 3: COMPOSITION/INFORMATION ON INGREDIENTS 3.2 Mixtures:
Synonyms: Mixed iron oxides, FexOy Formula: No data available Molecular Weight: No data available
Chemical Name CAS No. Concentration
Sucrose 57-50-7 <30%
Classification
Combustible Dust
Version 1.0 Revision Date: 2021-12-07
All other ingredients are non-hazardous or are hazardous to health or the environment and present below their cut-off levels according to the OSHA criteria. No other ingredients need to be disclosed according to the applicable regulations.
SECTION 4: FIRST-AID MEASURES
4.1 Description of Necessary First-Aid Measures:
Inhalation: Remove to fresh air. If person is not breathing give artificial respiration. If breathing becomes difficult give oxygen. Seek medical attention if necessary.
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Version 1.0 Revision Date: 2021-12-07
Skin: Wash with copious amounts of soap and water for at least fifteen minutes; removing contaminated clothing and shoes. Seek medical attention if necessary.
Eye: Flush with copious amounts of water for at least fifteen minutes. Remove contact lens after five minutes of washing, and then continue to irrigate the eyes. Ensure adequate flushing by separating the eyelids with protected fingers. Seek medical attention if necessary.
Ingestion: Rinse mouth with water. Do not induce vomiting unless told to do so by a medical professional. Contact the Poison Control Center or seek medical attention if necessary.
4.2 Most Important Symptoms/Effects, Acute and Delayed: See Section 2 and 11
4.3 Indication of any Immediate Medical Attention and Special Treatment Needed: No data available SECTION 5: FIRE-FIGHTING MEASURES
5.1 Suitable Extinguishing Media: Use water spray, carbon dioxide, dry chemical or alcohol-resistant foam. 5.2 Special Hazards Arising from the Chemical: Carbon oxides
5.3 Special Protective Actions for Fire-Fighters: Wear self-contained breathing apparatus and protective clothing if necessary.
SECTION 6: ACCIDENTAL RELEASE MEASURES
6.1 Personal Precautions, Protective Equipment and Emergency Procedures: Use personal protective equipment (see Section 8 for details). Ensure proper ventilation. Avoid dust formation. Avoid breathing dust.
6.2 Environmental Precautions: Do not let product enter drains or waterways or be discharged to the environment.
6.3 Methods and Materials for Containment and Cleaning Up: Do not dump into any sewers, on the ground or into any body of water. Wet an absorbent material to clean up spill. Place materials in a container for disposal according to location regulations. All disposal practices must be in compliance with all Federal, State and local laws and regulations (see Section 13). Regulations may vary in different locations. Waste characterizations and compliance with applicable laws are the responsibility solely of the waste generator. Keep in suitable, closed containers for disposal.
SECTION 7: HANDLING AND STORAGE
7.1 Precautions for Safe Handling: Avoid skin contact, eye contact and inhalation. Do not ingest. Avoid dust formation. Wear appropriate person protective equipment when handling (see Section 8). Use good laboratory practices when working with chemicals. Ensure proper ventilation. Wash hands after use.
7.2 Conditions for Safe Storage, including any Incompatibilities: Store upright in a tightly closed container in a dry and well ventilated area. Recommended storage temperature 2 – 8 °C , do not freeze.
SECTION 8: EXPOSURE CONTROLS/PERSONAL PROTECTION
8.1 Control Parameters:
Chemical CAS No.
Sucrose 57-50-1
Control Parameter
15 mg/m3 (total) 10 mg/m3 (total)
Basis
OSHA Table Z-1 Limits for Air Contaminants ACGIH Threshold Limit Value (TLV)
NIOSH Recommended Exposure Limit (REL)
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Version 1.0 Revision Date: 2021-12-07
Cal-OSHA Permissible Exposure Limits (PEL) for Chemical Contaminants
8.2 Appropriate Engineering Controls: Handle in accordance with good industrial hygiene and safety practices. Wash hands after use, before breaks and at the end of the day.
8.3 Individual Protection Measures, such as Personal Protective Equipment (PPE):
Eye/Face Protection: Safety glasses with side-shields. Eye protection equipment must be tested and approved by appropriate government standards such as NIOSH or EN166.
Skin Protection: Handle with gloves. Gloves should be inspected prior to use. Use proper glove removal technique (without touching glove’s outer surface) to avoid skin contact with this product. Dispose of contaminated gloves after use in accordance with applicable laws and good laboratory practices. Wash and dry hands upon glove removal.
Body Protection: Select body protection based on concentration and the amount of chemical that you will be working with. Impervious clothing should be worn.
Respiratory Protection: For nuisance exposures or exposures above applicable limits use respirators tested and approved under appropriate government standards such as NIOSH (US) or EN (EU).
SECTION 9: PHYSICAL AND CHEMICAL PROPERTIES AND SAFETY CHARACTERISTICS
Physical State Lyophilized Colour Brown Odour None Melting Point/Freezing Point 0C
Boiling Point or Initial Boiling Point and Boiling Range 100C
5 mg/m3 (resp)
ACGIH Threshold Limit Value (TLV)
NIOSH Recommended Exposure Limit (REL) OSHA Table Z-1 Limits for Air Contaminants Cal-OSHA Permissible Exposure Limits (PEL) for Chemical Contaminants
Flammability
Lower and Upper Explosion Limit/Flammability Limit Flash Point
Autoignition Temperature
Decomposition Temperature
pH
Kinematic Viscosity
Solubility
Partition Coefficient: n-octanol/water (log value) Vapour Pressure
Density and/or Relative Density
No data available No data available No data available No data available No data available 6-8
No data available No data available No data available No data available No data available
Page 3 of 6

Relative Vapor Density No data available
SECTION 10: STABILITY AND REACTIVITY
Version 1.0 Revision Date: 2021-12-07
10.1 Reactivity: No data available
10.2 Chemical Stability: Stable under normal temperatures and pressures.
10.3 Possibility of Hazardous Reactions: No data available
10.4 Conditions to Avoid: No data available
10.5 Incompatible Materials: Strong oxidizing agents
10.6 Hazardous Decomposition Products: No data available, see section 5 in the event of a fire. SECTION 11: TOXICOLOGICAL INFORMATION
11.1 Information on Toxicological Effects
Acute Toxicity: No data available
Skin Corrosion/Irritation: No data available
Serious Eye Damage/Eye Irritation: No data available Respiratory or Skin Sensitization: No data available Germ Cell Mutagenicity: No data available Carcinogenicity:
IARC: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by IARC.
ACGIH: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by ACGIH.
NTP: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by NTP.
OSHA: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by OSHA.
Reproductive Toxicity: No data available
Specific Target Organ Toxicity – Single Exposure: No data available
Specific Target Organ Toxicity – Repeated Exposure: No data available
Aspiration Hazard: No data available
Information on the Likely Routes of Exposure: Ingestion, skin, eyes, inhalation
Symptoms Related to the Physical, Chemical and Toxicological Characteristics: No data available Delayed and Immediate Effects and Chronic Effects from Short and Long-Term Exposure: No data available
Numerical Measures of Toxicity (such as acute toxicity estimates): No data available
Interactive Effects: No data available
Other information: To the best of our knowledge, the chemical, physical and toxicological properties of this mixture have not been thoroughly investigated.
Page 4 of 6

SECTION 12: ECOLOGICAL INFORMATION
12.1 Toxicity: No data available
12.2 Persistence and Degradability: No data available 12.3 Bioaccumulative Potential: No data available 12.4 Mobility in Soil: No data available
12.5 Other Adverse Effects: No data available SECTION 13: DISPOSAL CONSIDERATIONS
13.1 Disposal Methods:
Product: Dispose of in accordance with federal, state and local requirements.
Contaminated Packaging: Dispose of in accordance with federal, state and local requirements.
SECTION 14: TRANSPORTATION INFORMATION
DOT (US): Not a dangerous good IMDG: Not a dangerous good IATA: Not a dangerous good
SECTION 15: REGULATORY INFORMATION
15.1 Safety, Health and Environmental Regulations Specific for the Product in Question:
SARA 302 Components: No chemicals in this mixture are subject to the reporting requirements of SARA Title III, Section 302
SARA 313 Components: This mixture does not contain any chemicals with known CAS numbers that exceed the threshold reporting levels established by SARA Title III, Section 313.
SARA 311/312 Hazards: None
California Prop 65 Components: This product does not contain any chemicals known to the State of California to cause cancer, birth defects or any other reproductive harm.
SECTION 16: OTHER INFORMATION
16.1 Abbreviations and Acronyms:
ACGIH American Conference of Governmental Industrial Hygienists CAS Chemical Abstracts Service
CFR Code of Federal Regulations
DOT U.S. Department of Transportation
IATA International Air Transport Association IMDG International Maritime Dangerous Goods
NIOSH National Institute for Occupational Safety and Health OSHA Occupational Safety and Health Administration
PEL Permissible Exposure Limit
REL Recommended Exposure Limit
SARA Superfund Amendments and Reauthorization Act of 1986
SDS Safety Data Sheet TLV Threshold Limit Value U.S. United States
Version 1.0 Revision Date: 2021-12-07
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Version 1.0 Revision Date: 2021-12-07
Disclaimer/Statement of Liability – Seer, Inc. urges each recipient of this SDS to study it carefully and consult appropriate expertise, as necessary or appropriate, to become aware of and understand the data contained in this SDS and any hazards associated with the product. The information contained in this SDS applies to this specific material as supplied. It may not be valid for this material if it is used in combination with any other materials. The information herein is provided in good faith and believed to be accurate as of the preparation date shown above. This SDS has been prepared using information from sources considered technically reliable. It should not be relied upon as a product specification. The company makes no warranty of any kind, expressed or implied, concerning the safe use of this material in your process or in combination with other chemical substances. Regulatory requirements are subject to change and may differ between various locations. It is the user’s responsibility to ensure that its activities comply with all federal, state and local laws. Seer, Inc. shall not be held liable for any damage resulting from handling or from contact with the above product.
Page 6 of 6

SECTION 1: IDENTIFICATION
1.1 Product Identifier:
Product Number and Name: S55R1155, MS Peptide Control Index Number: Not Applicable
Registration Number: Not Applicable
CAS Number: Not Applicable
Safety Data Sheet
1.2 Recommended Use of the Chemical and Restrictions on Use: Laboratory chemicals, manufacture of substances
1.3 Supplier’s Details:
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
1.4 Emergency Phone Number: 650-453-0000 (M-F 9-5 PM PT)
SECTION 2: HAZARDS IDENTIFICATION
2.1 Classification of the Substance or Mixture:
GHS Classification in Accordance to 29 CFR 1910.1200: Not a hazardous substance or mixture 2.2 Label Element, Including Precautionary Statements:
Labeling GHS Labeling in accordance to 29 CFR 1910.1200: Pictogram(s): None
Signal Word: None
Hazard Statement(s): None
Precautionary Statement(s): None
2.3 Other Hazards which do not result in Classification: None SECTION 3: COMPOSITION/INFORMATION ON INGREDIENTS 3.2 Mixtures:
Synonyms: No data available Formula: No data available Molecular Weight: No data available
Chemical Name CAS No. Concentration Classification
All other ingredients are non-hazardous or are hazardous to health or the environment and present below their cut-off levels according to the OSHA criteria. No other ingredients need to be disclosed according to the applicable regulations.
For the full text of H-Statements and Abbreviations, see Section 16
Version 1.0 Revision Date: 2021-12-07
Formic Acid
64-18-6
0.1%
Flam. Liq. 3, H226; Acute Tox. 4, H302; Acute Tox. 3, H331; Skin Corr. 1A, H314; Eye Dam. 1, H318
Page 1 of 6

SECTION 4: FIRST-AID MEASURES
4.1 Description of Necessary First-Aid Measures:
Inhalation: Remove to fresh air. If person is not breathing give artificial respiration. If breathing becomes difficult give oxygen. Seek medical attention if necessary.
Skin: Wash with copious amounts of soap and water for at least fifteen minutes; removing contaminated clothing and shoes. Seek medical attention if necessary.
Eye: Flush with copious amounts of water for at least fifteen minutes. Remove contact lens after five minutes of washing, and then continue to irrigate the eyes. Ensure adequate flushing by separating the eyelids with protected fingers. Seek medical attention if necessary.
Ingestion: Rinse mouth with water. Do not induce vomiting unless told to do so by a medical professional. Contact the Poison Control Center or seek medical attention if necessary.
4.2 Most Important Symptoms/Effects, Acute and Delayed: See Section 2 and 11
4.3 Indication of any Immediate Medical Attention and Special Treatment Needed: No data available SECTION 5: FIRE-FIGHTING MEASURES
5.1 Suitable Extinguishing Media: Use water spray, carbon dioxide, dry chemical or alcohol-resistant foam. 5.2 Special Hazards Arising from the Chemical: No data available
5.3 Special Protective Actions for Fire-Fighters: Wear self-contained breathing apparatus and protective clothing if necessary.
SECTION 6: ACCIDENTAL RELEASE MEASURES
6.1 Personal Precautions, Protective Equipment and Emergency Procedures: Use personal protective equipment (see Section 8 for details). Avoid dust formation. Avoid breathing dust.
6.2 Environmental Precautions: Do not let product enter drains or waterways or be discharged to the environment.
6.3 Methods and Materials for Containment and Cleaning Up: Do not dump into any sewers, on the ground or into any body of water. Wet an absorbent material to clean up spill. Place materials in a container for disposal according to location regulations. All disposal practices must be in compliance with all Federal, State and local laws and regulations (see Section 13). Regulations may vary in different locations. Waste characterizations and compliance with applicable laws are the responsibility solely of the waste generator. Keep in suitable, closed containers for disposal.
SECTION 7: HANDLING AND STORAGE
7.1 Precautions for Safe Handling: Avoid skin contact, eye contact and inhalation. Do not ingest. Avoid dust formation. Wear appropriate person protective equipment when handling (see Section 8). Use good laboratory practices when working with chemicals. Wash hands after use.
7.2 Conditions for Safe Storage, including any Incompatibilities: Store upright in a tightly closed container in a dry and well ventilated area.
Page 2 of 6
Version 1.0 Revision Date: 2021-12-07

SECTION 8: EXPOSURE CONTROLS/PERSONAL PROTECTION
8.1 Control Parameters:
Chemical CAS No. Control Parameter Basis
Version 1.0 Revision Date: 2021-12-07
Formic Acid
64-18-6
5 ppm (TWA)
ACGIH Threshold Limit Values (TLV) NIOSH Recommended Exposure Limits (REL)
OSHA Occupational Exposure Limits – Table Z-1
Cal-OSHA Permissible Exposure Limit (PEL) for Chemical Contaminants
10 ppm (STEL)
ACGIH Threshold Limit Values (TLV) Cal-OSHA Permissible Exposure Limit (PEL) for Chemical Contaminants
8.2 Appropriate Engineering Controls: Handle in accordance with good industrial hygiene and safety practices. Wash hands after use, before breaks and at the end of the day.
8.3 Individual Protection Measures, such as Personal Protective Equipment (PPE):
Eye/Face Protection: Safety glasses with side-shields. Eye protection equipment must be tested and approved by appropriate government standards such as NIOSH or EN166.
Skin Protection: Handle with gloves. Gloves should be inspected prior to use. Use proper glove removal technique (without touching glove’s outer surface) to avoid skin contact with this product. Dispose of contaminated gloves after use in accordance with applicable laws and good laboratory practices. Wash and dry hands upon glove removal.
Body Protection: Select body protection based on concentration and the amount of chemical that you will be working with. Impervious clothing should be worn.
Respiratory Protection: For nuisance exposures or exposures above applicable limits use respirators tested and approved under appropriate government standards such as NIOSH (US) or EN (EU).
SECTION 9: PHYSICAL AND CHEMICAL PROPERTIES AND SAFETY CHARACTERISTICS
Physical State
Colour
Odour
Melting Point/Freezing Point
Boiling Point or Initial Boiling Point and Boiling Range Flammability
Lower and Upper Explosion Limit/Flammability Limit Flash Point
Lyophilized
No data available No data available No data available No data available No data available No data available No data available
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Version 1.0 Revision Date: 2021-12-07
Autoignition Temperature Decomposition Temperature pH
Kinematic Viscosity Solubility
Partition Coefficient: n-octanol/water (log value) Vapour Pressure
Density and/or Relative Density Relative Vapor Density
SECTION 10: STABILITY AND REACTIVITY
No data available
No data available No data available No data available No data available No data available No data available No data available No data available
10.1 Reactivity: No data available
10.2 Chemical Stability: Stable under normal temperatures and pressures.
10.3 Possibility of Hazardous Reactions: No data available
10.4 Conditions to Avoid: No data available
10.5 Incompatible Materials: No data available
10.6 Hazardous Decomposition Products: No data available, see section 5 in the event of a fire. SECTION 11: TOXICOLOGICAL INFORMATION
11.1 Information on Toxicological Effects
Acute Toxicity: No data available
Skin Corrosion/Irritation: No data available
Serious Eye Damage/Eye Irritation: No data available Respiratory or Skin Sensitization: No data available Germ Cell Mutagenicity: No data available Carcinogenicity:
IARC: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by IARC.
ACGIH: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by ACGIH.
NTP: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by NTP.
OSHA: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by OSHA.
Reproductive Toxicity: No data available
Specific Target Organ Toxicity – Single Exposure: No data available
Specific Target Organ Toxicity – Repeated Exposure: No data available Aspiration Hazard: No data available
Information on the Likely Routes of Exposure: Ingestion, skin, eyes, inhalation
Page 4 of 6

Version 1.0 Revision Date: 2021-12-07
Symptoms Related to the Physical, Chemical and Toxicological Characteristics: No data available Delayed and Immediate Effects and Chronic Effects from Short and Long-Term Exposure: No data available
Numerical Measures of Toxicity (such as acute toxicity estimates): No data available
Interactive Effects: No data available
Other information: To the best of our knowledge, the chemical, physical and toxicological properties of this mixture have not been thoroughly investigated.
SECTION 12: ECOLOGICAL INFORMATION
12.1 Toxicity: No data available
12.2 Persistence and Degradability: No data available 12.3 Bioaccumulative Potential: No data available 12.4 Mobility in Soil: No data available
12.5 Other Adverse Effects: No data available SECTION 13: DISPOSAL CONSIDERATIONS
13.1 Disposal Methods:
Product: Dispose of in accordance with federal, state and local requirements.
Contaminated Packaging: Dispose of in accordance with federal, state and local requirements.
SECTION 14: TRANSPORTATION INFORMATION
DOT (US): Not a dangerous good IMDG: Not a dangerous good IATA: Not a dangerous good
SECTION 15: REGULATORY INFORMATION
15.1 Safety, Health and Environmental Regulations Specific for the Product in Question:
SARA 302 Components: No chemicals in this mixture are subject to the reporting requirements of SARA Title III, Section 302
SARA 313 Components: This mixture does not contain any chemicals with known CAS numbers that exceed the threshold reporting levels established by SARA Title III, Section 313.
SARA 311/312 Hazards: None
California Prop 65 Components: This product does not contain any chemicals known to the State of California to cause cancer, birth defects or any other reproductive harm.
SECTION 16: OTHER INFORMATION
16.1 Abbreviations and Acronyms:
ACGIH Acute Tox. CAS CFR DOT Eye Dam. Flam. Liq.
American Conference of Governmental Industrial Hygienists Acute Toxicity
Chemical Abstracts Service
Code of Federal Regulations
U.S. Department of Transportation Eye Damage
Flammable Liquid
Page 5 of 6

H226 H302 H314 H318 H331 IATA IMDG NIOSH OSHA PEL REL SARA SDS Skin Corr. U.S.
Flammable liquid and vapour
Harmful if swallowed
Causes sever skin burns and eye damage
Causes serious eye damage
Toxic if inhaled
International Air Transport Association
International Maritime Dangerous Goods
National Institute for Occupational Safety and Health Occupational Safety and Health Administration Permissible Exposure Limit
Recommended Exposure Limit
Superfund Amendments and Reauthorization Act of 1986 Safety Data Sheet
Skin Corrosion
United States
Version 1.0 Revision Date: 2021-12-07
Disclaimer/Statement of Liability – Seer, Inc. urges each recipient of this SDS to study it carefully and consult appropriate expertise, as necessary or appropriate, to become aware of and understand the data contained in this SDS and any hazards associated with the product. The information contained in this SDS applies to this specific material as supplied. It may not be valid for this material if it is used in combination with any other materials. The information herein is provided in good faith and believed to be accurate as of the preparation date shown above. This SDS has been prepared using information from sources considered technically reliable. It should not be relied upon as a product specification. The company makes no warranty of any kind, expressed or implied, concerning the safe use of this material in your process or in combination with other chemical substances. Regulatory requirements are subject to change and may differ between various locations. It is the user’s responsibility to ensure that its activities comply with all federal, state and local laws. Seer, Inc. shall not be held liable for any damage resulting from handling or from contact with the above product.
Page 6 of 6

SECTION 1: IDENTIFICATION
1.1 Product Identifier:
Product Number and Name: S55R1156, MPE Control Index Number: Not Applicable
Registration Number: Not Applicable
CAS Number: Not Applicable
Safety Data Sheet
1.2 Recommended Use of the Chemical and Restrictions on Use: Laboratory chemicals, manufacture of substances
1.3 Supplier’s Details:
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
1.4 Emergency Phone Number: 650-453-0000 (M-F 9-5 PM PT)
SECTION 2: HAZARDS IDENTIFICATION
2.1 Classification of the Substance or Mixture:
GHS Classification in Accordance to 29 CFR 1910.1200: Not a hazardous substance or mixture 2.2 Label Element, Including Precautionary Statements:
Labeling GHS Labeling in accordance to 29 CFR 1910.1200: Pictogram(s): None
Signal Word: None
Hazard Statement(s): None
Precautionary Statement(s): None
2.3 Other Hazards which do not result in Classification: None SECTION 3: COMPOSITION/INFORMATION ON INGREDIENTS 3.2 Mixtures:
Synonyms: No data available Formula: No data available Molecular Weight: No data available
Chemical Name CAS No. Concentration Classification
All other ingredients are non-hazardous or are hazardous to health or the environment and present below their cut-off levels according to the OSHA criteria. No other ingredients need to be disclosed according to the applicable regulations.
For the full text of H-Statements and Abbreviations, see Section 16
Version 1.0 Revision Date: 2021-12-07
Formic Acid
64-18-6
0.1%
Flam. Liq. 3, H226; Acute Tox. 4, H302; Acute Tox. 3, H331; Skin Corr. 1A, H314; Eye Dam. 1, H318
Page 1 of 6

SECTION 4: FIRST-AID MEASURES
4.1 Description of Necessary First-Aid Measures:
Inhalation: Remove to fresh air. If person is not breathing give artificial respiration. If breathing becomes difficult give oxygen. Seek medical attention if necessary.
Skin: Wash with copious amounts of soap and water for at least fifteen minutes; removing contaminated clothing and shoes. Seek medical attention if necessary.
Eye: Flush with copious amounts of water for at least fifteen minutes. Remove contact lens after five minutes of washing, and then continue to irrigate the eyes. Ensure adequate flushing by separating the eyelids with protected fingers. Seek medical attention if necessary.
Ingestion: Rinse mouth with water. Do not induce vomiting unless told to do so by a medical professional. Contact the Poison Control Center or seek medical attention if necessary.
4.2 Most Important Symptoms/Effects, Acute and Delayed: See Section 2 and 11
4.3 Indication of any Immediate Medical Attention and Special Treatment Needed: No data available SECTION 5: FIRE-FIGHTING MEASURES
5.1 Suitable Extinguishing Media: Use water spray, carbon dioxide, dry chemical or alcohol-resistant foam. 5.2 Special Hazards Arising from the Chemical: No data available
5.3 Special Protective Actions for Fire-Fighters: Wear self-contained breathing apparatus and protective clothing if necessary.
SECTION 6: ACCIDENTAL RELEASE MEASURES
6.1 Personal Precautions, Protective Equipment and Emergency Procedures: Use personal protective equipment (see Section 8 for details). Avoid dust formation. Avoid breathing dust.
6.2 Environmental Precautions: Do not let product enter drains or waterways or be discharged to the environment.
6.3 Methods and Materials for Containment and Cleaning Up: Do not dump into any sewers, on the ground or into any body of water. Wet an absorbent material to clean up spill. Place materials in a container for disposal according to location regulations. All disposal practices must be in compliance with all Federal, State and local laws and regulations (see Section 13). Regulations may vary in different locations. Waste characterizations and compliance with applicable laws are the responsibility solely of the waste generator. Keep in suitable, closed containers for disposal.
SECTION 7: HANDLING AND STORAGE
7.1 Precautions for Safe Handling: Avoid skin contact, eye contact and inhalation. Do not ingest. Avoid dust formation. Wear appropriate person protective equipment when handling (see Section 8). Use good laboratory practices when working with chemicals. Wash hands after use.
7.2 Conditions for Safe Storage, including any Incompatibilities: Store upright in a tightly closed container in a dry and well ventilated area.
Page 2 of 6
Version 1.0 Revision Date: 2021-12-07

SECTION 8: EXPOSURE CONTROLS/PERSONAL PROTECTION
8.1 Control Parameters:
Chemical CAS No. Control Parameter Basis
Version 1.0 Revision Date: 2021-12-07
Formic Acid
64-18-6
5 ppm (TWA)
ACGIH Threshold Limit Values (TLV) NIOSH Recommended Exposure Limits (REL)
OSHA Occupational Exposure Limits – Table Z-1
Cal-OSHA Permissible Exposure Limit (PEL) for Chemical Contaminants
10 ppm (STEL)
ACGIH Threshold Limit Values (TLV) Cal-OSHA Permissible Exposure Limit (PEL) for Chemical Contaminants
8.2 Appropriate Engineering Controls: Handle in accordance with good industrial hygiene and safety practices. Wash hands after use, before breaks and at the end of the day.
8.3 Individual Protection Measures, such as Personal Protective Equipment (PPE):
Eye/Face Protection: Safety glasses with side-shields. Eye protection equipment must be tested and approved by appropriate government standards such as NIOSH or EN166.
Skin Protection: Handle with gloves. Gloves should be inspected prior to use. Use proper glove removal technique (without touching glove’s outer surface) to avoid skin contact with this product. Dispose of contaminated gloves after use in accordance with applicable laws and good laboratory practices. Wash and dry hands upon glove removal.
Body Protection: Select body protection based on concentration and the amount of chemical that you will be working with. Impervious clothing should be worn.
Respiratory Protection: For nuisance exposures or exposures above applicable limits use respirators tested and approved under appropriate government standards such as NIOSH (US) or EN (EU).
SECTION 9: PHYSICAL AND CHEMICAL PROPERTIES AND SAFETY CHARACTERISTICS
Physical State
Colour
Odour
Melting Point/Freezing Point
Boiling Point or Initial Boiling Point and Boiling Range Flammability
Lower and Upper Explosion Limit/Flammability Limit Flash Point
Lyophilized
No data available No data available No data available No data available No data available No data available No data available
Page 3 of 6

Version 1.0 Revision Date: 2021-12-07
Autoignition Temperature Decomposition Temperature pH
Kinematic Viscosity Solubility
Partition Coefficient: n-octanol/water (log value) Vapour Pressure
Density and/or Relative Density Relative Vapor Density
SECTION 10: STABILITY AND REACTIVITY
No data available
No data available No data available No data available No data available No data available No data available No data available No data available
10.1 Reactivity: No data available
10.2 Chemical Stability: Stable under normal temperatures and pressures.
10.3 Possibility of Hazardous Reactions: No data available
10.4 Conditions to Avoid: No data available
10.5 Incompatible Materials: No data available
10.6 Hazardous Decomposition Products: No data available, see section 5 in the event of a fire. SECTION 11: TOXICOLOGICAL INFORMATION
11.1 Information on Toxicological Effects
Acute Toxicity: No data available
Skin Corrosion/Irritation: No data available
Serious Eye Damage/Eye Irritation: No data available Respiratory or Skin Sensitization: No data available Germ Cell Mutagenicity: No data available Carcinogenicity:
IARC: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by IARC.
ACGIH: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by ACGIH.
NTP: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by NTP.
OSHA: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by OSHA.
Reproductive Toxicity: No data available
Specific Target Organ Toxicity – Single Exposure: No data available
Specific Target Organ Toxicity – Repeated Exposure: No data available Aspiration Hazard: No data available
Information on the Likely Routes of Exposure: Ingestion, skin, eyes, inhalation
Page 4 of 6

Version 1.0 Revision Date: 2021-12-07
Symptoms Related to the Physical, Chemical and Toxicological Characteristics: No data available Delayed and Immediate Effects and Chronic Effects from Short and Long-Term Exposure: No data available
Numerical Measures of Toxicity (such as acute toxicity estimates): No data available
Interactive Effects: No data available
Other information: To the best of our knowledge, the chemical, physical and toxicological properties of this mixture have not been thoroughly investigated.
SECTION 12: ECOLOGICAL INFORMATION
12.1 Toxicity: No data available
12.2 Persistence and Degradability: No data available 12.3 Bioaccumulative Potential: No data available 12.4 Mobility in Soil: No data available
12.5 Other Adverse Effects: No data available SECTION 13: DISPOSAL CONSIDERATIONS
13.1 Disposal Methods:
Product: Dispose of in accordance with federal, state and local requirements.
Contaminated Packaging: Dispose of in accordance with federal, state and local requirements.
SECTION 14: TRANSPORTATION INFORMATION
DOT (US): Not a dangerous good IMDG: Not a dangerous good IATA: Not a dangerous good
SECTION 15: REGULATORY INFORMATION
15.1 Safety, Health and Environmental Regulations Specific for the Product in Question:
SARA 302 Components: No chemicals in this mixture are subject to the reporting requirements of SARA Title III, Section 302
SARA 313 Components: This mixture does not contain any chemicals with known CAS numbers that exceed the threshold reporting levels established by SARA Title III, Section 313.
SARA 311/312 Hazards: None
California Prop 65 Components: This product does not contain any chemicals known to the State of California to cause cancer, birth defects or any other reproductive harm.
SECTION 16: OTHER INFORMATION
16.1 Abbreviations and Acronyms:
ACGIH Acute Tox. CAS CFR DOT Eye Dam. Flam. Liq.
American Conference of Governmental Industrial Hygienists Acute Toxicity
Chemical Abstracts Service
Code of Federal Regulations
U.S. Department of Transportation Eye Damage
Flammable Liquid
Page 5 of 6

H226 H302 H314 H318 H331 IATA IMDG NIOSH OSHA PEL REL SARA SDS Skin Corr. U.S.
Flammable liquid and vapour
Harmful if swallowed
Causes sever skin burns and eye damage
Causes serious eye damage
Toxic if inhaled
International Air Transport Association
International Maritime Dangerous Goods
National Institute for Occupational Safety and Health Occupational Safety and Health Administration Permissible Exposure Limit
Recommended Exposure Limit
Superfund Amendments and Reauthorization Act of 1986 Safety Data Sheet
Skin Corrosion
United States
Version 1.0 Revision Date: 2021-12-07
Disclaimer/Statement of Liability – Seer, Inc. urges each recipient of this SDS to study it carefully and consult appropriate expertise, as necessary or appropriate, to become aware of and understand the data contained in this SDS and any hazards associated with the product. The information contained in this SDS applies to this specific material as supplied. It may not be valid for this material if it is used in combination with any other materials. The information herein is provided in good faith and believed to be accurate as of the preparation date shown above. This SDS has been prepared using information from sources considered technically reliable. It should not be relied upon as a product specification. The company makes no warranty of any kind, expressed or implied, concerning the safe use of this material in your process or in combination with other chemical substances. Regulatory requirements are subject to change and may differ between various locations. It is the user’s responsibility to ensure that its activities comply with all federal, state and local laws. Seer, Inc. shall not be held liable for any damage resulting from handling or from contact with the above product.
Page 6 of 6

SECTION 1: IDENTIFICATION
1.1 Product Identifier:
Synonyms: No data available Formula: No data available Molecular Weight: No data available
Chemical Name CAS No.
Potassium EDTA 25102-12-9
Concentration Classification
<1% Skin Irr. 2, H315; Eye Irr. 2, H319; STOT SE 3, H335
Safety Data Sheet
Product Number and Name: S55R1157, Plasma Control and S55R1181, Plasma Sample Index Number: Not Applicable
Registration Number: Not Applicable
CAS Number: Not Applicable
1.2 Recommended Use of the Chemical and Restrictions on Use: Laboratory chemicals, manufacture of substances
1.3 Supplier’s Details:
Name: Seer, Inc.
Address: 3800 Bridge Parkway, Suite 102 Redwood City, CA 94065 Phone: 650-453-0000
1.4 Emergency Phone Number: 650-453-0000 (M-F 9-5 PM PT)
SECTION 2: HAZARDS IDENTIFICATION
2.1 Classification of the Substance or Mixture:
GHS Classification in Accordance to 29 CFR 1910.1200: Not a hazardous substance or mixture 2.2 Label Element, Including Precautionary Statements:
Labeling GHS Labeling in accordance to 29 CFR 1910.1200: Pictogram(s): None
Signal Word: None
Hazard Statement(s): None
Precautionary Statement(s): None
2.3 Other Hazards which do not result in Classification: Human source material SECTION 3: COMPOSITION/INFORMATION ON INGREDIENTS
3.2 Mixtures:
Version 1.0 Revision Date: 2021-12-07
All other ingredients are non-hazardous or are hazardous to health or the environment and present below their cut-off levels according to the OSHA criteria. No other ingredients need to be disclosed according to the applicable regulations.
For the full text of H-Statements and Abbreviations, see Section 16.
Page 1 of 6

SECTION 4: FIRST-AID MEASURES
4.1 Description of Necessary First-Aid Measures:
Inhalation: Remove to fresh air. If person is not breathing give artificial respiration. If breathing becomes difficult give oxygen. Seek medical attention if necessary.
Skin: Wash with copious amounts of soap and water for at least fifteen minutes; removing contaminated clothing and shoes. Seek medical attention if necessary.
Eye: Flush with copious amounts of water for at least fifteen minutes. Remove contact lens after five minutes of washing, and then continue to irrigate the eyes. Ensure adequate flushing by separating the eyelids with protected fingers. Seek medical attention if necessary.
Ingestion: Rinse mouth with water. Do not induce vomiting unless told to do so by a medical professional. Seek medical attention if necessary.
4.2 Most Important Symptoms/Effects, Acute and Delayed: See Section 2 and 11
4.3 Indication of any Immediate Medical Attention and Special Treatment Needed: No data available SECTION 5: FIRE-FIGHTING MEASURES
5.1 Suitable Extinguishing Media: Use water spray, carbon dioxide, dry chemical or alcohol-resistant foam. 5.2 Special Hazards Arising from the Chemical: Carbon oxides, sodium oxides
5.3 Special Protective Actions for Fire-Fighters: Wear self-contained breathing apparatus and protective clothing if necessary.
SECTION 6: ACCIDENTAL RELEASE MEASURES
6.1 Personal Precautions, Protective Equipment and Emergency Procedures: Use personal protective equipment (see Section 8 for details). Ensure proper ventilation. Avoid dust formation. Avoid breathing dust. 6.2 Environmental Precautions: No data available
6.3 Methods and Materials for Containment and Cleaning Up: Do not dump into any sewers, on the ground or into any body of water. Wet an absorbent material to clean up spill. Place materials in a container for disposal according to location regulations. All disposal practices must be in compliance with all Federal, State and local laws and regulations (see Section 13). Regulations may vary in different locations. Waste characterizations and compliance with applicable laws are the responsibility solely of the waste generator. Keep in suitable, closed containers for disposal.
SECTION 7: HANDLING AND STORAGE
7.1 Precautions for Safe Handling: Avoid skin contact, eye contact and inhalation. Do not ingest. Avoid dust formation. Wear appropriate person protective equipment when handling (see Section 8). Use good laboratory practices. Ensure proper ventilation. Wash hands after use.
7.2 Conditions for Safe Storage, including any Incompatibilities: Store upright in a tightly closed container in a dry and well ventilated area. Recommended storage temperature 2 – 8 °C.
SECTION 8: EXPOSURE CONTROLS/PERSONAL PROTECTION
8.1 Control Parameters: Contains no substances with occupational exposure limit values.
8.2 Appropriate Engineering Controls: Handle in accordance with good industrial hygiene and safety practices. Wash hands after use, before breaks and at the end of the day.
Page 2 of 6
Version 1.0 Revision Date: 2021-12-07

Version 1.0 Revision Date: 2021-12-07
8.3 Individual Protection Measures, such as Personal Protective Equipment (PPE):
Eye/Face Protection: Safety glasses with side-shields. Eye protection equipment must be tested and approved by appropriate government standards such as NIOSH or EN166.
Skin Protection: Handle with gloves. Gloves should be inspected prior to use. Use proper glove removal technique (without touching glove’s outer surface) to avoid skin contact with this product. Dispose of contaminated gloves after use in accordance with applicable laws and good laboratory practices. Wash and dry hands upon glove removal.
Body Protection: Select body protection based on concentration and the amount of material that you will be working with. Impervious clothing should be worn.
Respiratory Protection: For nuisance exposures or exposures above applicable limits use respirators tested and approved under appropriate government standards such as NIOSH (US) or EN (EU).
SECTION 9: PHYSICAL AND CHEMICAL PROPERTIES AND SAFETY CHARACTERISTICS
Physical State
Colour
Odour
Melting Point/Freezing Point
Boiling Point or Initial Boiling Point and Boiling Range Flammability
Lower and Upper Explosion Limit/Flammability Limit Flash Point
Autoignition Temperature
Decomposition Temperature
pH
Kinematic Viscosity
Solubility
Partition Coefficient: n-octanol/water (log value) Vapour Pressure
Density and/or Relative Density
Relative Vapor Density
SECTION 10: STABILITY AND REACTIVITY
Lyophilized
No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available No data available
10.1 Reactivity: No data available
10.2 Chemical Stability: Stable under normal temperatures and pressures.
10.3 Possibility of Hazardous Reactions: No data available
10.4 Conditions to Avoid: No data available
10.5 Incompatible Materials: Strong oxidizing agents
10.6 Hazardous Decomposition Products: No data available, see section 5 in the event of a fire.
Page 3 of 6

SECTION 11: TOXICOLOGICAL INFORMATION
11.1 Information on Toxicological Effects
Acute Toxicity: No data available
Skin Corrosion/Irritation: No data available
Serious Eye Damage/Eye Irritation: No data available Respiratory or Skin Sensitization: No data available Germ Cell Mutagenicity: No data available Carcinogenicity:
IARC: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by IARC.
ACGIH: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by ACGIH.
NTP: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by NTP.
OSHA: No component of this product present at levels greater than or equal to 0.1% is identified as probable, possible or confirmed human carcinogen by OSHA.
Reproductive Toxicity: No data available
Specific Target Organ Toxicity – Single Exposure: No data available
Specific Target Organ Toxicity – Repeated Exposure: No data available
Aspiration Hazard: No data available
Information on the Likely Routes of Exposure: Ingestion, skin, eyes, inhalation
Symptoms Related to the Physical, Chemical and Toxicological Characteristics: No data available Delayed and Immediate Effects and Chronic Effects from Short and Long-Term Exposure: No data available
Numerical Measures of Toxicity (such as acute toxicity estimates): No data available
Interactive Effects: No data available
Other information: To the best of our knowledge, the chemical, physical and toxicological properties of this mixture have not been thoroughly investigated.
SECTION 12: ECOLOGICAL INFORMATION
12.1 Toxicity: No data available
12.2 Persistence and Degradability: No data available 12.3 Bioaccumulative Potential: No data available 12.4 Mobility in Soil: No data available
12.5 Other Adverse Effects: No data available SECTION 13: DISPOSAL CONSIDERATIONS
13.1 Disposal Methods:
Product: Dispose of in accordance with federal, state and local requirements.
Contaminated Packaging: Dispose of in accordance with federal, state and local requirements.
Page 4 of 6
Version 1.0 Revision Date: 2021-12-07

SECTION 14: TRANSPORTATION INFORMATION
DOT (US): Not a dangerous good IMDG: Not a dangerous good IATA: Not a dangerous good
SECTION 15: REGULATORY INFORMATION
15.1 Safety, Health and Environmental Regulations Specific for the Product in Question:
SARA 302 Components: No chemicals in this mixture are subject to the reporting requirements of SARA Title III, Section 302
SARA 313 Components: This mixture does not contain any chemicals with known CAS numbers that exceed the threshold reporting levels established by SARA Title III, Section 313.
SARA 311/312 Hazards: None
California Prop 65 Components: This product does not contain any chemicals known to the State of California to cause cancer, birth defects or any other reproductive harm.
SECTION 16: OTHER INFORMATION
16.1 Abbreviations and Acronyms:
Version 1.0 Revision Date: 2021-12-07
ACGIH CAS CFR DOT Eye Irr. H315 H319 H335 IATA IMDG NIOSH OSHA SARA SDS Skin Irr. STOT SE U.S.
American Conference of Governmental Industrial Hygienists Chemical Abstracts Service
Code of Federal Regulations
U.S. Department of Transportation
Eye Irritation
Causes skin irritation
Causes serious eye irritation
May cause respiratory irritation
International Air Transport Association
International Maritime Dangerous Goods
National Institute for Occupational Safety and Health Occupational Safety and Health Administration Superfund Amendments and Reauthorization Act of 1986 Safety Data Sheet
Skin Irritation
Specific Target Organ Toxicity (Single Exposure)
United States
Disclaimer/Statement of Liability – Seer, Inc. urges each recipient of this SDS to study it carefully and consult appropriate expertise, as necessary or appropriate, to become aware of and understand the data contained in this SDS and any hazards associated with the product. The information contained in this SDS applies to this specific material as supplied. It may not be valid for this material if it is used in combination with any other materials. The information herein is provided in good faith and believed to be accurate as of the preparation date shown above. This SDS has been prepared using information from sources considered technically reliable. It should not be relied upon as a product specification. The company makes no
Page 5 of 6

Version 1.0 Revision Date: 2021-12-07
warranty of any kind, expressed or implied, concerning the safe use of this material in your process or in combination with other chemical substances. Regulatory requirements are subject to change and may differ between various locations. It is the user’s responsibility to ensure that its activities comply with all federal, state and local laws. Seer, Inc. shall not be held liable for any damage resulting from handling or from contact with the above product.
Page 6 of 6

USER GUIDE
ProteographTM Analysis Suite
seer.bio

Notice
© 2021 Seer, Inc. All rights reserved. Information in this document is subject to change without notice. Seer assumes no responsibility for any errors or omissions in this document. Duplication and/or reproduction of all or any portion of this document without the express written consent of Seer is strictly forbidden. Seer does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.
Nothing contained herein shall constitute any warranty, express or implied, as to the performance of any products described herein, or any warranties of merchantability, fitness for a particular purpose or non-infringement. The use of products described herein is subject to certain restrictions as set forth in the applicable terms and conditions of sale or license accompanying the purchase of such product and any written agreements between Seer and user. Seer may refer to products or services offered by other companies by their brand names or company names solely for clarity and does not claim any rights in those third party marks or names. All products and services described herein are intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s).
Failure to completely read and explicitly follow all of the instructions contained herein may result in damage to the product(s), injury to persons, including to users or others, and damage to other property, and will void any warranty applicable to the product(s). Seer does not assume any liability arising out of the improper use of the product(s) described herein (including parts thereof or software).
BUYER IS NOT LICENSED OR AUTHORIZED TO, AND AGREES NOT TO, USE ANY SEER PRODUCT FOR ANY CLINICAL OR DIAGNOSTIC PURPOSES.
Notice
Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5) 2

Revision history
DOCUMENT DATE
CF-1003 B October (PAS version 1.5) 2021
DESCRIPTION OF CHANGE
Per Proteograph Analysis Suite Release Notes (CF-1018 A)
New analyses to visualize differences in peptide/protein group intensities between samples and groups
• New interactive table containing peptide/protein group intensities across samples/groups
• New heatmap plot for visualizing peptide/protein group intensities across samples/groups
New analysis to identify peptide/protein groups with significantly different intensities between groups (e.g., healthy vs. disease samples)
• Added new “Group analysis” sections to ‘Analysis’ section
• Guided comparison setup providing data filtering, normalization, imputation,
and statistical test options
• Toggle for viewing only ‘Significant Peptides/Proteins’ in dataset
• Interactive plots and tables for exploratory expression analysis of significantly
regulated targets with dynamic fold-change and p-value options
• New group analysis plots to visualize peptides/protein groups with statistically
different intensities
– Volcano plot – fold-change vs. statistical significance with coloring options
to highlight proteins-of-interest
– Coverage viewer – Amino acid sequence coverage by peptides display,
including PTM detection
– Clustered heatmap – visualizing peptide/protein group intensities across
samples/groups with rows (peptide/protein groups) and columns (samples)
ordered using hierarchical clustering
– Protein-protein interaction – Visualization of PPIs (STRING db) of
significant proteins
– Intensity box plots – Compare significant peptide/protein group intensities
between groups
Changes to plot visualizations
• Added ability to export plot source data to .csv files
• Improved plot rendering speeds
• Added user preferences to modify plots
New analysis protocols
• Integration of DIA-NN database search engine
– Pre-installed DIA-NN library-based protocol (DIANN – System Provided
DIA Protocol)
– Expanded Seer human plasma spectral library file (4,011 protein groups;
62,687 precursors)
– Optional in silico predicted library-free protocol
Revision history
Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5) 3

Revision history
DOCUMENT
DATE
DESCRIPTION OF CHANGE
Changes to results summary
• Simplified peptide and protein group results tables
– Panel level summary
– NP level summary
Changes to help content
• Updated user guide
• Indexed online help
• Tooltips
New data file management
• New AutoUploader application allows automatic data transfer from LC-MS system to PAS account
Initial release
CF-1003 A (PAS version 1.0)
May 2021
Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5) 4

Contents
Notice
Revision history Contents
Chapter 1 Welcome to PAS
Access the PAS application
Tour of the PAS application Sidebar menu
Top bar and User Account menu Work with PAS tables
Show or hide table columns
Add custom columns
Sort a table
Filter a table; search for a specific item
Control how many items are shown per table page Navigate among table pages
Access item details and/or sub-items Set color preferences in PAS graphs
Get help with PAS
Manage your user profile
Input files
Plate map file format
Sample description file format
Output files
Quality control Application settings
Change the appearance of the user interface Configure application settings
Configure two-factor authentication for yourself Configure default display settings for analysis results
User management
Users and Permissions page Add a user
Edit a user
Delete a user
Chapter 2 Analysis Setup
Analysis setup workflows
Setup workflow: Add a plate
Add one or more MS data files
Add the plate map file
Specify plate information
Add a sample description file (optional) Add the samples to a project
Start the analysis
Setup workflow: Link to a plate
Review the MS data files to be linked a plate Add the plate map file
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Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5)
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Specify plate information
Add a sample description file (optional) Add the samples to a project
Start the analysis
Setup workflow: Select samples or controls for analysis Analyze selected samples
Analyze controls only
Chapter 3 Analysis Results
Access analysis results
Review analysis results Data visualization Analysis Summary tab
Open an analysis’s Analysis Summary tab Summary section
Protein Group Counts section
Set Protein Group Counts preferences Peptide Counts section
Set Peptide Counts preferences
Distribution of Detected Proteins in Plasma Proteome section
Set Distribution of Detected Proteins in Plasma Proteome preferences Protein Group Overlap Sets section
Set Protein Group Overlap Sets preferences Sample Comparability section
Set Sample Comparability preferences Analysis Metrics tab
Open an analysis’s Analysis Metrics tab Intensities section
Set Intensities preferences Plate Map Grid section
Set Plate Map Grid preferences Lamppost Proteins’ Concentration section
Set Lamppost Proteins’ Concentration preferences PCA Analysis section
Change the PCA Analysis color scheme
Peptide Counts Distribution and Protein Group Counts Distribution sections
Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles sections
Set Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles preferences Hierarchical Clustering section
QC Charts tab
Open and filter an analysis’s QC Charts tab
Set QC Charts preferences
Manage user-defined and calculated control limits
Define and use user-defined control limits Define and use calculated control limits Delete a calculated control limit date range Exclude a sample
Annotate control charts Add an annotation Edit an annotation
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Delete an annotation
Generate reports of control results
Download summarized control results
Generate a detailed PDF report of control results
Analysis Output Files tab
Chapter 4 Analysis Interpretation
Open an analysis’s Group Analysis tab
Export raw data to a file
View a raw protein group data heatmap Set up and start a group analysis
Specify the quantitation level and grouping of samples Filter out (exclude) samples and groups
Filter out (exclude) proteins or peptides
Normalize values and impute sparse or missing values Select the statistical test and the groups to compare
Group Analysis tab Raw Data section
Clustered Heatmap section Volcano section
Coverage section
Filtered PPI Network section Enrichment section
Box Plots section
Chapter 5 Data Management
Plates and samples
Plates page Review a plate
Edit a plate
Delete a plate Plate Samples section
Add samples to an existing plate Add sample descriptions
Edit sample information
Delete a sample from a plate
Plate Grid section
Edit or delete samples in wells
Upload a custom file containing sample information
Projects
Projects page
Add a project
Delete a project Sample List section
Add samples to a project Analyses
Analyses page
Download an analysis log
Download an analysis’s protein groups and peptides results Edit an analysis
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Delete one or more analyses
MS data files
Data Files page
Create a folder
Upload MS data files
Move MS data files
Rename MS data files or folders
Delete MS data files or folders
Download and install the Seer AutoUploader application
Analysis protocols Protocols page
View an analysis protocol’s search engine parameters Upload an analysis protocol
Copy an analysis protocol
Download an analysis protocol
Delete an analysis protocol
Glossary
Index
Technical Support
Contact Information
Telephone
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Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5)
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Chapter 1
Welcome to PAS
Introduces you to the Seer ProteographTM Analysis Suite (PAS) software application, part of the Seer ProteographTM Product Suite.
With this dedicated software solution, you can process, analyze, and visualize proteomics data sets generated by liquid chromatography-mass spectrometry (LC-MS). PAS includes an integrated search engine for identification and annotation of LC-MS data.

Chapter 1 Welcome to PAS Access the PAS application
Access the PAS application
To access the PAS application, point your web browser to pas.seer.software. Compatible browsers include Chrome, Chromium, Edge, Firefox, and Safari.
When prompted to log in, enter your username and password. In the future, if you configure two-factor authentication, you will also need to enter a code generated by an authenticator app on your mobile device. (For details for setting up two-factor authentication, see Configure two-factor authentication for yourself (page 19).)
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Chapter 1 Welcome to PAS
Tour of the PAS application
Tour of the PAS application
The PAS application window has several main parts.
Sidebar menu
Use the sidebar menu to access PAS functionality and data.
A Plates — For importing sample metadata from the Proteograph Assay
method and associated MS data files. See Plates and samples (page 76).
B Projects — For grouping Proteograph Assay plates at the experimental
project level and submitting data analysis jobs. See Projects (page 83).
C Analyses — For accessing data analysis jobs, data analysis results, and data
visualizations. See Analyses (page 86).
D Data Files — For accessing the repository of MS data files and managing
your data. See MS data files (page 89).
E Analysis Protocol — For accessing a collection of database search analysis
protocols. See Analysis protocols (page 92).
F Users — (Admin only) For viewing, adding, editing, and deleting users. See
User management (page 21).
G Help — For accessing PAS documentation including the user guide (PDF),
web-based Help system, and videos. See Get help with PAS (page 14).
Top bar and User Account menu
The top bar of the PAS application window has just one component, the User Account menu, at the far right. To open the menu, select your username.
A B
C D
E
Sidebar menu
Button to expand and collapse the sidebar menu
Top bar
User Account menu, accessible from your username
Page with table items. For general table techniques, see Work with PAS tables (next page).
NOTE
When the sidebar menu is collapsed, the top bar — including your username — is hidden.
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Chapter 1 Welcome to PAS
Tour of the PAS application
A B C
D
User Profile — For managing your user information, such as your telephone number. See Manage your user profile (page 14).
Appearance — For selecting a light or dark theme for the PAS user interface. See Change the appearance of the user interface (page 19).
Settings — For configuring various application settings, including which DDA and DIA protocols will be used by default for data analysis. See Configure application settings (page 19).
Logout — Logs you out of PAS.
Work with PAS tables
Information in PAS is organized into tables. For example, the Projects page (page 83) offers a table of all
projects, while the Users and Permissions page (page 21) offers a table of all PAS users. Use the following techniques when working with tables.
Show or hide table columns
Some tables offer a Show/Hide list from which you can show and hide columns by selecting and clearing checkboxes.
Add custom columns
You can add custom columns to the Plate Samples section (page 78) and Sample List section (page 84). Any custom column you add to one of these tables is available for the other table. You can show and hide custom columns like any other column.
To add a custom column:
1. Select Show/Hide, scroll to the bottom of the list, and select Add Custom to open the Add Custom
Field dialog.
2. Complete the fields.
– Custom Name — A unique name for this custom field, within this table and with no spaces.
– Description — The description of the custom field.
– Notes — Additional information about the custom field.
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Chapter 1 Welcome to PAS Tour of the PAS application
3. Select Create.
The custom field (column) appears at the bottom of the Show/Hide column with the prefix custom_.
Sort a table
Sort table items by selecting the heading of the column you want to sort by. PAS sorts in descending order by default. To reverse the order, select the heading again. To turn off sorting entirely, select the heading one more time.
Filter a table; search for a specific item
Filter a table to show only specific items — and to find a specific item — by typing a string of characters in the Search field. As you type, PAS refreshes the table to show only matching items. To show all items again, clear the Search field.
Control how many items are shown per table page
To control how many table items PAS shows per page, select an option from the Items per page list, located at the lower right below the table.
Navigate among table pages
Depending on how many items are shows per page, some tables may be broken into several pages. To navigate among the pages, use the left and right arrows located at the lower left below the table.
Access item details and/or sub-items
Some tables offer access to item details and/or related sub-items. To access an item’s details or its sub-items, select that item’s row. For example, on the Projects page, selecting a project row to access its related samples.
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Chapter 1 Welcome to PAS
Tour of the PAS application
Set color preferences in PAS graphs
Many Preferences dialogs for PAS graphs offer controls with which you can set colors to suit your preferences. These controls open a color picker from which you can select a color.
Get help with PAS
To set a color preference:
1. Select the color control, such as Graph Colors as shown here, to open the color picker.
2. Select a color on the color spectrum or enter a color’s hexadecimal value.
3. Click outside color picker to close it.
PAS offers many in-application resources where you can learn how to get the most out of it.
1. On the sidebar menu, select Help to open the Help page.
2. Select the resource you’re interested in: PAS web-based Help, the PDF of the user guide, or training videos.
Manage your user profile
1. On the User Account menu, select User Profile to open the User Profile page.
2. Edit the fields as needed. (Depending on your role and organization, the fields may vary.)
– User Profile — Edit your first name, last name, and phone number.
– Tenant Info — Edit information about your organization and your address.
3. Select Save.
A B
Selected item
Table of sub-items associated with the selected item
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Chapter 1 Welcome to PAS
Input files
Input files
PAS accepts the following files as input for analysis.
• Analysis protocol (.xml, .json) — (Optional) The parameters for an MS database search. PAS includes preinstalled analysis protocols for both data-dependent acquisition (DDA) and data-independent acquisition (DIA) data files.
• MS data files (.raw, .wiff, .wiff.scan) — The results of MS analysis for each sample or control in a plate. Each sample or control is associated with one MS data file.
• Plate map file (.csv) — The location of each sample in a plate with information on each sample, control, nanoparticle, and peptide.
• Sample description file (.csv) — Metadata for each sample in a plate, such as sample name and IDs, type, species, and condition.
Plate map file format
The ProteographTM Instrument Control Software (ICS) generates the plate map file (.csv). All columns are prefilled except tor MS file name, which you must define.
COLUMN DESCRIPTION
MS file name The name of the MS data file, including extension (for example, EXP20101_ 2020ms0321X83_A.raw)
Sample name A unique identifier for the sample, typically the biological sample name1
Sample ID A unique identifier for the sample1
Well location The column and row of the well the sample occupies
Nanoparticle The nanoparticle name (nanoparticle 1–5)
Nanoparticle ID The nanoparticle lot (kit ID)
Control The control type: Process Control, Digestion Control, MPE Control, or MS Peptide Control
Control ID The control lot
Instrument name The name of the liquid handler that converted the samples into peptides
Date sample The date the method ended preparation
Sample volume The volume of sample in the indicated well2
Peptide concentration The concentration of peptide in the well2
Peptide mass sample The mass of peptide in the well2
Recon volume The volume of Peptide Reconstitution Buffer added to the well2
Kit ID The ID of the assay kit used to convert the samples into peptides
Plate ID A unique identifier for the plate
Plate Name A descriptive name for the plate
1The sample name links the plate map and sample description files, while the sample ID groups the nanoparticles in an assay. 2The file shows the numeric value only, without unit of measure.
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Chapter 1 Welcome to PAS
Input files
Sample description file format
The sample description file (.csv) contains the following information about each sample in a plate. The file can also include custom (user-defined) columns. These columns must include the prefix custom_.
Table 1. Columns in a sample description file
COLUMN DESCRIPTION
Sample Name A unique identifier for the sample, typically the biological sample name
Sample Type The type of sample, such as plasma or tissue lysate
Species The species (human or mouse) from which the sample was collected
Description A description of the sample
Sample Receipt Date The date your laboratory received the sample
Sample Collection Date The date the sample was collected
Condition The categorical group the sample belongs to
Biological Replicate The biological replicate number
Technical Replicate The technical replicate number
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Chapter 1 Welcome to PAS Output files
Output files
An analysis generates several results files, which record search results for each sample in .txt and .xml formats.
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Chapter 1 Welcome to PAS Quality control
Quality control
A plate includes prepared samples and the following controls for quality control (QC) purposes. The control results provide insight into the variation and reproducibility of experiments and LC-MS analysis.
• Process Control — A reference sample added before protein corona formation.
• Digestion Control — A reference sample added before trypsin digestion.
• MPE Control — Reference peptides added before desalting cleanup.
• MS Peptide Control — Reference peptides added before LC-MS analysis.
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Chapter 1 Welcome to PAS Application settings
Application settings
You can configure several PAS application settings, including the default analysis protocols for controls and samples. You can also change the appearance of the PAS user interface. These settings are global and apply to all analyses and pages. Finally, you can configure two-factor authentication for yourself.
Change the appearance of the user interface
1. On the User Account menu, select Appearance to open the Appearance page.
2. Select the theme you want to use:
– Light (default) — Makes the background of the user interface white.
– Dark — Makes the background of the user interface black.
3. Select Save.
Configure application settings
Follow these steps to configure PAS application settings. See also Configure two-factor authentication for
yourself (below).
1. On the User Account menu, select Settings to open the Settings page.
2. In the Settings section, configure settings as needed.
– Default Analysis Protocol — Select the DDA-based and DIA-based analysis protocols you want to use for controls and for samples.
– Remove MS data files when plate is deleted — Select either:
. No (default) to have PAS retain the MS data files linked to the plate.
. Yes to have PAS delete the MS data files linked to the plate.
– Receive email notifications on analysis updates — Select either:
. Yes (default) to have PAS send you an email whenever an analysis status changes.
. No to have PAS not send emails about analysis updates.
3. Select Save.
Configure two-factor authentication for yourself
You can configure PAS to require two-factor authentication when you log in. That means that PAS will prompt not only for your username and password, but also for a generated authentication code.
Before continuing, you will need to have already installed an authentication app on your mobile device. PAS is compatible with many such apps, including Google Authenticator, Duo Mobile, 1Password, Auth, and Microsoft Authenticator.
1. On the User Account menu, select Settings to open the Settings page.
2. In the Two-factor Authentication section, select Use Authenticator App to open the Authenticator
verification dialog.
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Chapter 1 Welcome to PAS Application settings
3. Using the authenticator app on your mobile device, either scan the QR code or enter the key shown on- screen into the authenticator app.
4. In PAS, enter the generated code.
5. Select Submit and then select OK to close the success message.
Configure default display settings for analysis results
In addition to configuring PAS application settings (see Configure application settings (previous page)), you can also configure display settings for analysis results. These display settings determine which analysis results are
NOTE
Notice that the Use Authenticator App button now reads Disable Authenticator App Security. To turn two-factor authentication off, follow the same steps as above, select that button, and follow the on-screen prompts.
shown
and how they are grouped and sorted. The settings are global and apply to all analyses.
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Select any analysis.
3. Below the Analyses table, locate and select Display Settings to open the Display Settings dialog.
4. Configure settings as needed.
– Group by — Select an option for grouping protein group and peptide counts.
– Sort by — Select an option for sorting data on the Analysis Summary tab.
– — Select or clear checkboxes to show or hide wells. Scroll to see all wells.
– Hide Controls — Set the toggle key to ON to hide controls.
– Visualization graphs — Select each toggle key to ON or OFF to show or hide the corresponding graph.
5. Select Continue to apply the settings.
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Chapter 1 Welcome to PAS
User management
User management
If you are a PAS administrator, you can add, edit, and delete users.
Users and Permissions page
If you are an Admin, use the Users and Permissions page to manage PAS users. • To open this page, select Users on the sidebar menu.
Toolbar items
• Add User — Select to add a new user. See Add a user (below).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item
(page 13). Table columns
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
Name — The user’s name.
Email — The user’s email address.
Role — The user’s role, which grants access to specific PAS functionality.
– User — Can add plates, create projects, create analysis protocols, view MS data files, and view results files.
– Admin — In addition to User functionality, can also manage users. Group — The group or groups the user is assigned to.
Status — The user’s status (e.g., Confirmed, meaning acceptance of the invitation to join PAS). (Edit) — Select to edit the selected user. See Edit a user (next page).
• • •


• •
1. On the sidebar menu, select Users to open the Users and Permissions page.
2. Select Add User to open the Invite User dialog.
3. Complete the fields. Required fields are marked on-screen with an asterisk.
– Username — Enter a unique identifier for the user.
– Email — Enter the user’s email address.
NOTE
– Use group assignments to limit user access to specific plates, projects, and analyses.
– Members of a user group can access and view the plates, projects, and analyses of everyone in the group.
(Delete) — Select to delete the selected user. See Delete a user (next page). Add a user
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Chapter 1 Welcome to PAS User management
– Role — From the list, select the user’s role: User (the default) or Admin.
– User Groups — (For a user of User role) From the list, select one or more existing user groups. To
add a new group, enter its name.
4. Select Send.
The user will be sent an email invitation with the assigned username, a temporary password, and a link to
PAS.
Edit a user
1. On the sidebar menu, select Users to open the Users and Permissions page.
2. Find the user you want to edit and select (Edit) to open the Edit User dialog.
3. Edit the fields as needed.
4. Select Save.
Delete a user
1. On the sidebar menu, select Users to open the Users and Permissions page.
2. Find the user you want to delete and select (Delete).
3. Select OK to confirm.
NOTE
. Use group assignments to limit user access to specific plates, projects, and analyses.
. Members of a user group can access and view the plates, projects, and analyses of everyone in
the group.
. By default, PAS excludes the user from all groups.
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Chapter 2
Analysis Setup
Offers step-by-step guidance for different setup workflows for getting ready for analysis.

Chapter 2 Analysis Setup Analysis setup workflows
Analysis setup workflows
PAS offers several workflows for getting ready for data analysis. To set up a new plate and initiate a new analysis, follow:
• Setup workflow: Add a plate (next page) — This is the most straightforward setup workflow. Begin on the Plates page and add a plate.
• Setup workflow: Link to a plate (page 28) — Begin on the Data Files page, add MS data files, and then link the files to a plate.
To analyze existing plate data, follow:
• Setup workflow: Select samples or controls for analysis (page 31) — Begin on the Projects page to analyze samples. Choose this workflow when you have more than one plate whose samples you want to analyze in a single analysis. You can also choose this workflow when you want to reanalyze samples.
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Chapter 2 Analysis Setup Setup workflow: Add a plate
Setup workflow: Add a plate
When you set up analysis by adding a plate, PAS guides you through the workflow with the Add Plate dialog. In this workflow, you add a new plate to PAS and then add samples to a new or existing project. Depending on your choices during the workflow, the analysis will start immediately or will be deferred for later.
To begin this workflow:
1. On the sidebar menu, select Plates to open the Plates page.
2. Select Add Plate to open the Add Plate dialog.
Add one or more MS data files
In the MSData Files section, you add one or more MS data files.
1. Select the MS data files.
– To add a single file, select Files to open the Add Files dialog.
– To add multiple files, select Folder to open the Add Folder dialog.
2. Either drag the file or folder into the drag-and-drop area or use Browse to navigate to and select it.
3. Select Add.
4. Review the selected files.
– To remove a file, select (Delete).
– To remove all files, select Clear.
5. Select Next to advance.
Add the plate map file
In the Plate Map File section, you add a plate map file, which specifies the locations of samples.
1. If you don’t have a plate map file, create one before continuing.
a. Select the on-screen link from which you can download an example plate map file (.csv).
b. Open the file and edit it as needed.
The MS file name, Sample ID, and Plate ID columns are required. (See Plate map file format (page 15) for detailed descriptions of the columns in the file.)
c. Save as a .csv file.
2. Select Add File or Add to open the Add File dialog.
NOTE
Supported file formats are .raw, wiff, or .wiff.scan. Supported folders are RAW and D.
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Chapter 2 Analysis Setup Setup workflow: Add a plate
3. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
4. Select Add.
5. Select Next to advance.
Specify plate information
In the Plate ID and Name section, you link the MS data files to a new or existing plate.
1. Do either of the following:
– To link to an existing plate, select Use Existing Plate, and then select a plate from the Select Existing Plate list.
– To set up a new plate, complete the fields.
. Plate ID — A unique identifier for the plate.
. Plate Name — A descriptive name for the plate.
2. Select Next to advance.
Add a sample description file (optional)
In the Sample Description File section, you upload metadata for each sample in the plate.
1. Select Add or Add File to open the Add Files dialog.
2. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
3. Select Add.
4. Select Next to advance.
Add the samples to a project
In the Add to Project section, you add samples to a new or existing project. Depending on your choices, the analysis will start immediately or will be deferred for later.
1. Create or select a project:
– To create a new project, select New Project, enter a project name, and select Add.
– To use an existing project, select it from the Select Project list.
2. Select or clear the applicable checkboxes. (To defer analysis, clear both checkboxes.)
– Analyze samples after addition — Select to analyze samples.
– Analyze controls after addition — Select to analyze controls.
3. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual
precursor ion.
NOTE
This part of the workflow is optional. To skip it, select Next to advance.
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Chapter 2 Analysis Setup Setup workflow: Add a plate
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
4. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
5. Select Add Plate, and then select Close.
– If you had selected either or both Analyze… checkboxes earlier, the analysis starts immediately.
– If you deferred analysis, you must start it manually. See Start the analysis (below).
Start the analysis
If you deferred analysis during the setup workflow, follow these steps to start the analysis.
1. On the sidebar menu, select Projects to open the Projects page.
2. Select the applicable project.
3. Select one of the following options:
– Analyze — Opens the Analysis dialog from which to analyze all selected samples in the project.
– Analyze Controls — Opens the Analyze Controls dialog from which to analyze the controls only.
4. If you are analyzing all selected samples, in the Analysis Name field, enter a name for the analysis.
5. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
6. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
7. In the Description field, enter a description of the analysis.
8. In the Notes field, optionally enter any additional information about the analysis.
9. If you are analyzing all selected samples and want to exclude the controls, select the Exclude controls checkbox.
10. If you are analyzing only controls, under Analysis Name Pattern, review the MS data file name format and list of controls to analyze.
11. Select Start, and then select OK.
The samples or controls are queued for analysis.
12. On the sidebar menu, select Analyses to open the Analyses page.
13. Confirm that the new analysis appears on the Analyses page.
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Chapter 2 Analysis Setup Setup workflow: Link to a plate
Setup workflow: Link to a plate
When you set up analysis by linking to a plate, PAS guides you through the workflow with the Link to Plate dialog. In this workflow, you link MS data files and associated sample information to a new or existing plate. Depending on your choices during the workflow, the analysis will start immediately or will be deferred for later.
To begin this workflow:
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Select the folder that holds the files you want to work with.
3. Select the checkbox of each MS data file to include in the analysis. Each MS data file represents one sample.
4. Select Link to Plate to open the Link to Plate dialog.
Review the MS data files to be linked a plate
In the MSData Files section, you review the selected MS data files to be linked to a plate.
1. Review the selected MS data files.
– To remove a file, select its (Delete) button.
– To remove all files, select Clear.
2. Select Next to advance.
Add the plate map file
In the Plate Map File section, you add a plate map file, which specifies the locations of samples.
1. If you don’t have a plate map file, create one before continuing.
a. Select the on-screen link from which you can download an example plate map file (.csv).
b. Open the file and edit it as needed.
The MS file name, Sample ID, and Plate ID columns are required. (See Plate map file format (page 15) for detailed descriptions of the columns in the file.)
c. Save as a .csv file.
2. Select Add File or Add to open the Add File dialog.
3. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
NOTE
If you have not already uploaded the MS data files you want to work with, follow the steps in Upload MS data files (page 90) before starting this workflow.
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Chapter 2 Analysis Setup
Setup workflow: Link to a plate
4. Select Add.
5. Select Next to advance.
Specify plate information
In the Plate ID and Name section, you link the MS data files to a new or existing plate.
1. Do either of the following:
– To link to an existing plate, select Use Existing Plate, and then select a plate from the Select Existing Plate list.
– To set up a new plate, complete the fields.
. Plate ID — A unique identifier for the plate.
. Plate Name — A descriptive name for the plate.
2. Select Next to advance.
Add a sample description file (optional)
In the Sample Description File section, you upload metadata for each sample in the plate.
1. Select Add or Add File to open the Add Files dialog.
2. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
3. Select Add.
4. Select Next to advance.
Add the samples to a project
In the Add to Project section, you add the samples to a new or existing project. Depending on your choices, the analysis will start immediately or will be deferred for later.
1. Create or select a project:
– To create a new project, select New Project, enter a project name, and select Add.
– To use an existing project, select it from the Select Project list.
2. Select or clear the applicable checkboxes. (To defer analysis, clear both checkboxes.)
– Analyze samples after addition — Select to analyze samples.
– Analyze controls after addition — Select to analyze controls.
3. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual
precursor ion.
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
NOTE
This part of the workflow is optional. To skip it, select Next to advance.
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Chapter 2 Analysis Setup Setup workflow: Link to a plate
4. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
5. Select Add Plate, and then select Close.
– If you had selected either or both Analyze… checkboxes earlier, the analysis starts immediately.
– If you deferred analysis, you must start it manually. See Start the analysis (below).
Start the analysis
If you deferred analysis during the setup workflow, follow these steps to start the analysis.
1. On the sidebar menu, select Projects to open the Projects page.
2. Select the applicable project.
3. Select one of the following options:
– Analyze — Opens the Analysis dialog from which to analyze all selected samples in the project.
– Analyze Controls — Opens the Analyze Controls dialog from which to analyze the controls only.
4. If you are analyzing all selected samples, in the Analysis Name field, enter a name for the analysis.
5. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
6. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
7. In the Description field, enter a description of the analysis.
8. In the Notes field, optionally enter any additional information about the analysis.
9. If you are analyzing all selected samples and want to exclude the controls, select the Exclude controls checkbox.
10. If you are analyzing only controls, under Analysis Name Pattern, review the MS data file name format and list of controls to analyze.
11. Select Start, and then select OK.
The samples or controls are queued for analysis.
12. On the sidebar menu, select Analyses to open the Analyses page.
13. Confirm that the new analysis appears on the Analyses page.
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Chapter 2 Analysis Setup Setup workflow: Select samples or controls for analysis
Setup workflow: Select samples or controls for analysis
The Projects page is the starting point for the sample selection method of analysis setup.
Choose this workflow when you have more than one plate whose samples you want to analyze in a single
analysis. You can also use this workflow to reanalyze samples. See Analyze selected samples (below). Use this workflow also to analyze controls only. See Analyze controls only (next page).
NOTE
For this workflow, PAS must already contain the applicable plate and MS data files in a project.
Figure 1. Projects page (left) and Analysis dialog (right)
Analyze selected samples
1. On the sidebar menu, select Projects to open the Projects page.
2. Select the applicable project.
3. Select the checkbox of each sample to analyze.
4. Select Analyze to open the Analysis dialog.
5. In the Analysis Name field, enter a name for the analysis.
6. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method),
select a protocol.
7. In the Description field, enter a description of the analysis.
8. In the Notes field, optionally enter any additional information about the analysis.
9. If you want to exclude the controls, select the Exclude controls checkbox.
10. Select Start, and then select OK. The samples are queued for analysis.
11. On the sidebar menu, select Analyses to open the Analyses page.
12. Confirm that the new analysis appears on the Analyses page.
A Selected samples
B Analyze button
C Analysis dialog
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Chapter 2 Analysis Setup Setup workflow: Select samples or controls for analysis
Analyze controls only
1. On the sidebar menu, select Projects to open the Projects page.
2. Select the applicable project.
3. Select samples, and then select Analyze Controls to open the Analyze Controls dialog.
4. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
5. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
6. In the Description field, enter a description of the analysis.
7. In the Notes field, enter any additional information about the analysis.
8. Under Analysis Name Pattern, review the MS data file name format and the list of controls to analyze.
9. Select Start, and then select OK.
The samples are queued for analysis.
10. On the sidebar menu, select Analyses to open the Analyses page.
11. Confirm that the new analysis is listed.
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Chapter 3
Analysis Results
Describes analysis results (exclusive of Group Analysis) and offers step-by-step guidance for working with them.

Chapter 3 Analysis Results Access analysis results
Access analysis results
Access analysis results on the Analyses page, where you can review data in a variety of graphs and download results files. The results of the selected analysis are arranged in up to five tabs, each presenting a subset: Analysis Summary, Analysis Metrics, Group Analysis, QC Charts, and Analysis Output Files.
NOTE
Depending on the selected analysis, the QC Charts tab might not be shown.
Figure 2. Analyses page
A Select an analysis C
B Select tabs to view subsets of the analysis’s
results D
Download the analysis’s protein groups and peptide results
A results graph
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34

Chapter 3 Analysis Results Review analysis results
Review analysis results
1. On the sidebar menu, select Analyses to open the Analyses page.
2. From the Status list, select Completed.
3. To apply additional filters, select options from any of the following lists:
– Project — Shows analyses for specified projects.
– Plate — Shows analyses for specified plates.
– Controls/Samples — Shows analyses for controls only or samples only.
4. Select an analysis.
5. On the Analysis Summary tab, compare samples and review a summary of the analysis, counts of peptides and protein groups, the dynamic range distribution of detected proteins, sample overlap, and sample correlation. To learn more about this tab, begin at Analysis Summary tab (page 37).
6. On the Analysis Metrics tab, review the intensities, sample clusters, nanoparticle counts, and other QC metrics. To learn more about this tab, begin at Analysis Metrics tab (page 44).
7. If the analysis included controls, select the QC Charts tab to review the control results. To learn more about this tab, begin at QC Charts tab (page 53).
8. On the Analysis Output Files tab, review results files.
9. (Optional) Use Protein Group / Peptide Results to download the analysis’s protein groups and
peptide results. See Download an analysis’s protein groups and peptides results (page 87).
NOTE
If you select multiple analyses, PAS does not show an analysis summary or results files and, instead, groups all data in the graphs on the remaining tabs.
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Chapter 3 Analysis Results Data visualization
Data visualization
Several tabs of the Analyses page (page 86) are divided into expandable and collapsible sections. Some sections include a menu for downloading graph data as a .svc, .png, or .csv file. Sections with many graphs include scroll arrows for accessing all the graphs.
Figure 3. Example section
A Scroll arrows and page numbers to move through all graphs
B Arrow to expand or collapse the section
C Menu for downloading data in the section
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Chapter 3 Analysis Results Analysis Summary tab
Analysis Summary tab
An analysis’s Analysis Summary tab (on the Analyses page) offers an overall view of analysis results, organized into sections.
For some sections, you can modify labels, reorganize layouts, and otherwise adjust display preferences. These modifications are temporary and apply only to the select analysis. When you leave the Analyses page, each section returns to the default view. (To configure display preferences for all analyses in PAS, see Configure default display settings for analysis results (page 20).)
Open an analysis’s Analysis Summary tab
1. On the sidebar menu, select Analyses to open the Analyses page.
2. From the Status list, select Completed.
3. Select an analysis to open its analysis results.
4. Select the Analysis Summary tab.
Summary section
The Summary section shows the following information.
• Analysis name — The name of the analysis.
• Number of samples — The number of samples analyzed.
• Peptides across — The total number of distinct peptides across samples.
• Run types — The analysis protocol type, either DDA or DIA.
• Protein group across — The total number of distinct protein groups across samples.
• Peptide average — The average number of peptides per sample.
• Analysis protocol — The name of the analysis protocol applied to the analysis.
• Protein group average — The average number of protein groups per sample.
Protein Group Counts section
The Protein Group Counts section graphs the number of proteins in each sample. The y-axis plots the number of identified protein groups and the x-axis plots each well. Three lines compare protein group trends for the plate:
• The individual line traces the total number of protein groups observed in each sample.
• The cumulative line traces the cumulative number of protein groups observed with each successive sample. For example, the A3 value reflects the number of protein groups detected at least one time among A1, A2, and A3.
• The common line traces the proteins in common for each successive sample. For example, the A3 value reflects the number of proteins in common with A1, then A2.
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
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Chapter 3 Analysis Results Analysis Summary tab
Dots along each line identify values for each well.
• Hover over a dot on the line graph to view the exact value.
• Select a dot in the legend to hide the corresponding line.
• Hover over a dot in the legend to hide the lines corresponding to the other dots.
To customize this section for the selected analysis, see Set Protein Group Counts preferences (below). Figure 4. Line graph showing protein group counts
Set Protein Group Counts preferences
You can customize the appearance of the Protein Group Counts section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Summary tab. (See Open an analysis’s Analysis Summary tab (previous page).)
2. In the Protein Group Counts section, select (Settings) to open the Preferences dialog.
3. Set preferences as needed.
– X Tick Label — Select the label to show along the x-axis, e.g., Sample Name, Plate Name, Sample ID.
– Y Axis Range — Select the range for the y-axis.
. Min is 0 and Max Data Dependent — The minimum value is set at 0 and the maximum value depends on data.
. Min and Max Data Dependent — Both the minimum and maximum values depend on data.
. User Defined — Enter the minimum and maximum values.
4. Select Continue to apply the settings.
Peptide Counts section
The Peptide Counts section graphs the number of peptides in each sample. The y-axis plots the peptide count, and the x-axis plots each sample. You can update the x-axis label, but the values remain the same. Hover over a dot on the line graph to view the exact value.
To customize this section for the selected analysis, see Set Peptide Counts preferences (next page).
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Chapter 3 Analysis Results Analysis Summary tab
Figure 5. Line graph showing peptide counts
Set Peptide Counts preferences
You can customize the appearance of the Peptide Counts section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Summary tab. (See Open an analysis’s Analysis Summary tab (page 37).)
2. In the Peptide section, select (Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
– X Tick Label — Select the label to show along the x-axis, e.g., Sample Name, Plate Name, Sample ID.
– Y Axis Range — Select the range for the y-axis.
. Min is 0 and Max Data Dependent — The minimum value is set at 0 and the maximum value depends on data.
. Min and Max Data Dependent — Both the minimum and maximum values depend on data.
. User Defined — Enter the minimum and maximum values.
4. Select Continue to apply the settings.
Distribution of Detected Proteins in Plasma Proteome section
The Distribution of Detected Proteins in Plasma Proteome section shows the dynamic range of proteins identified in each sample compared to a deep reported human plasma proteome index.1 The n-value equals the number of proteins detected in the sample that were also detected in the index.
The x-axis plots the number of identified proteins ranked by database intensity. The y-axis plots the intensity calculated in the database using the logarithm base 10 (log10) function. Each protein appears as a circle on the plot.
• Hover over a circle to view the name of the protein and the exact intensity values.
• Use the scroll arrows and numbers to move through all the graphs.
• Select or clear wells in the Samples list to show or hide the corresponding graphs.
• Enter a keyword or term in the Search field to find specific graphs.
• Annotate proteins you want to highlight, as shown in red in the following figure.
To customize this section for the selected analysis, see Set Distribution of Detected Proteins in Plasma
Proteome preferences (next page).
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Chapter 3 Analysis Results Analysis Summary tab
Figure 6. Graph comparing the proteins detected in sample A3 to the plasma proteome
1Keshishian, Hasmik, Michael W. Burgess, Michael A. Gillette, Philipp Mertins, Karl R. Clauser, D. R. Mani, Eric W. Kuhn, et al., “Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury,’ 14, no. 9 Molecular & Cellular Proteomics (September 2015): 2375–2393, https://doi.org/10.1074/mcp.M114.046813.
Set Distribution of Detected Proteins in Plasma Proteome preferences
You can customize the appearance of the Distribution of Detected Proteins in Plasma Proteome section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Summary tab. (See Open an analysis’s Analysis Summary tab (page 37).)
2. In the Distribution of Detected Proteins in Plasma Proteome section, select (Settings) to open the
Preferences dialog.
3. Adjust the settings as you prefer.
– Graph Colors — Use the color picker to select graph colors. (See Set color preferences in PAS graphs (page 14).)
– Page Chart Layout — Select an option for how many graphs appear on a page and the layout. For example, the 2 × 2 option shows four graphs per page, two down and two across.
– Quantiles — Adjust the frequency distribution. The default quantiles are 0.25, 0.5, and 0.75.
. To add a quantile, select Add and enter its value.
. To modify existing quantiles, update the values in each field.
. To delete a quantile, select (Delete).
– Proteins — Annotate proteins of interest by entering their names, separated by commas (e.g., P35579,F5H7Y6,Q5VZ73). The dots representing the annotated proteins will appear on each graph in red with the protein names above.
4. Select Continue to apply the settings.
Protein Group Overlap Sets section
The Protein Group Overlap Sets section is divided into two bar graphs and a matrix that together show protein group intersections. The Within Samples checkbox shows intersection size and protein group count as standalone graphs for each sample with a dot representing the MS data file.
• Hover over a vertical bar to view the intersection size for the group of samples as an integer and the percentage of the total it represents.
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Chapter 3 Analysis Results Analysis Summary tab
• Hover over a horizontal bar to view the sample and the exact number of protein groups it contains.
• Select or clear wells in the Samples list to show or hide the corresponding bars.
To customize this section for the selected analysis, see Set Protein Group Overlap Sets preferences (below). Figure 7. Graphs and a matrix show protein group overlaps
A Intersection Size bar graph C Matrix
B Protein Group Count bar graph
Set Protein Group Overlap Sets preferences
You can customize the appearance of the Protein Group Overlap Sets section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Summary tab. (See Open an analysis’s Analysis Summary tab (page 37).)
2. In the Protein Group Overlap Sets section, select (Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
– Horizontal Bar Position — Select an orientation for the graph.
. Left — The graph is positioned left.
. Right — The graph is positioned right.
. None — The graph is hidden.
– Vertical Height Rate — Enter a value for the relative bar height in the graph.
– MS file’s name length — Enter the character limit for the MS data file name.
– Display Top N Intersection — Select which bars appear on the graph.
. All — Shows intersection sizes for all samples.
. 4 — Shows the intersection sizes of the top four largest samples only.
. 8 — Shows the intersection sizes of the top eight largest samples only.
. 16 — Shows the intersection sizes of the top 16 largest samples only.
. 32 — Shows the intersection sizes of the top 32 largest samples only.
– Display Percentage — Select to show percentages on top of each bar in the Intersection Size graph.
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Chapter 3 Analysis Results Analysis Summary tab
– Page Chart Layout — Select an option for how many graphs appear on a page and the layout. For example, the 2 × 2 option shows four graphs per page, two down and two across.
By default, this section consolidates information for all samples into two bar graphs and a matrix for easy comparison. You can divide these elements into graphs for individual samples and change the page layout accordingly.
– — Set colors for the various parts of the graph, such as for the vertical and horizontal bars. Use the techniques in Set color preferences in PAS graphs (page 14).
4. Select Continue to apply the settings. Sample Comparability section
The Sample Comparability section shows the degree of statistical correlation between samples based on the Pearson correlation coefficient (PCC) and the similarity in protein groups between samples based on the Jaccard Index, which measures the linear correlation of data. You can switch between the PCC and Jaccard index.
Each matrix is color-coded for easy reference. Samples on the green end of the spectrum have high correlation. Samples on the red end of the spectrum have low correlation.
To customize this section for the selected analysis, see Set Sample Comparability preferences (below). Figure 8. A color-coded matrix shows sample comparability data using PCC (left) or the Jaccard index (right)
Set Sample Comparability preferences
You can temporarily customize the appearance of the Sample Comparability section (above). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Summary tab. (See Open an analysis’s Analysis Summary tab (page 37).)
2. In the Sample Compatibility section, select (Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
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Chapter 3 Analysis Results Analysis Summary tab
– Similarity Score — To change how sample intensity data are compared, select either:
. Pearson’s correlation coefficient — Shows data calculated by normalizing the covariance
measurement.
. Jaccard index — Shows data calculated by dividing the intersection size by the union size.
– Color Labels By — To change the matrix label colors, select an option, e.g., Sample Name, Sample ID, Plate Name. To not use colors for labels, select Disabled.
– Label Font Size — Select the point size text of the label.
4. Select Continue to apply the settings.
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Chapter 3 Analysis Results Analysis Metrics tab
Analysis Metrics tab
An analysis’s Analysis Metrics tab (on the Analyses page) shows the QC metrics for an analysis result, organized into sections. The metrics indicate how well an analysis method performed.
For some sections, you can modify labels, reorganize layouts, and otherwise adjust display preferences. These modifications are temporary and apply only to the select analysis. When you leave the Analyses page, each section returns to the default view. (To configure display preferences for all analyses in PAS, see Configure default display settings for analysis results (page 20).)
Open an analysis’s Analysis Metrics tab
1. On the sidebar menu, select Analyses to open the Analyses page.
2. From the Status list, select Completed.
3. Select an analysis to open its analysis results.
4. Select the Analysis Metrics tab.
Intensities section
The Intensities section graphs the protein and peptide intensities and the distribution of protein sequence coverage for each sample, including the coefficient of variation (CV). You can update the default chart type, a density plot, to a violin plot.
On a density plot, the x-axis plots intensity and the y-axis plots density.
• Move the pointer along a curve to view the exact intensity value at each point in the curve.
• Select a sample in the legend to hide the corresponding line.
• Hover over a sample in the legend to hide the lines corresponding to the other samples.
On a violin plot, the sample appears along the x-axis and the y-axis plots intensity. Box plots represent quantile ranges with box plots with density on either end. Red dots represent outliers.
• Hover over a box plot to view the quantile for the sample.
• Hover over a dot to view the exact outlier value.
To customize this section for the selected analysis, see Set Intensities preferences (next page).
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
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Chapter 3 Analysis Results Analysis Metrics tab
Figure 9. Density plot (left) and violin plot (right) showing the intensity distribution for a sample
Set Intensities preferences
You can temporarily customize the appearance of the Intensities section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Metrics tab. (See Open an analysis’s Analysis Metrics tab (previous page).)
2. In the Intensities section, select (Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
– Page Chart Layout — Select an option for how many graphs appear on a page and the layout. For example, the 2 × 2 option shows four graphs per page, two down and two across.
– Chart Type — Select an option.
. Density plot — Shows the full distribution of data for each sample as a continuous curve.
. Violin plot — Shows data for each sample as quartiles with the full distribution of data.
4. Select Continue to apply the settings.
Plate Map Grid section
The Plate Map Grid section shows metrics for each sample in the format of 96-well plates. Each plate represents one of the following metrics. Hover over a well to view the value. Alternatively, you can consolidate these data into a single table with one column for each metric.
• Protein group counts — The number of protein groups identified per well.
• Peptide counts — The number of peptides identified per well.
• Peptide quant mass — The mass of peptide in the well as calculated by the peptide quantification assay.
• Miscleavage rate — The fraction of peptides identified as having missed cleavages based on the maximum allowable missed cleavages set in the analysis protocol.
• Oxidation ratio — The fraction of peptides identified with methionine oxidation.
• ID rate — The rate at which an MS/MS scan is converted into a database peptide identification.
To customize this section for the selected analysis, see Set Plate Map Grid preferences (next page).
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Chapter 3 Analysis Results Analysis Metrics tab
Figure 10. Grids for each metric showing results for each sample
Set Plate Map Grid preferences
You can temporarily customize the appearance of the Plate Map Grid section (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Metrics tab. (See Open an analysis’s Analysis Metrics tab (page 44).)
2. In the Plate Map Grid section, select (Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
– Graph Types — Select each toggle key to show or hide a graph or table column (depending on the Display Type).
– Scaling — Select Each graph or Each type scaling for reviewing multiple plates.
– Display Type — Select an option:
. Plate Map Grid — Shows each metric in a separate grid.
. Table — Shows the protein group counts, peptide counts, and other metrics in one table.
– Page Chart Layout — Select an option for how many graphs appear on a page and the layout. For
example, the 2 × 2 option shows four graphs per page, two down and two across.
4. Select Continue to apply the settings.
Lamppost Proteins’ Concentration section
The Lamppost Proteins’ Concentration section graphs the intensity of landmark proteins in each sample. The x-axis plots each well and plate and the y-axis plots log10 intensity.
Five lines compare intensities for the proteins HP, APOC3, PROS1, F11, and ALB. Dots along each line identify the intensity value for each protein in the sample.
• Hover over a dot on the line graph to view the exact value for all five proteins.
• Select a dot in the legend to hide the corresponding line.
• Hover over a dot on the legend to hide the lines corresponding to the other dots.
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Chapter 3 Analysis Results Analysis Metrics tab
To customize this section for the selected analysis, see Set Lamppost Proteins’ Concentration preferences (below). Specifically, you can add, edit, and delete proteins.
Figure 11. Line graph showing intensities for landmark proteins
Set Lamppost Proteins’ Concentration preferences
You can temporarily customize the appearance of the Lamppost Proteins’ Concentration section (previous page). Specifically, you can add, edit, and delete proteins to use instead of the default QC landmark proteins. The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Metrics tab. (See Open an analysis’s Analysis Metrics tab (page 44).)
2. In the Lamppost Proteins Concentration section, select (Settings) to open the Lamppost Proteins
dialog.
3. To add a protein or group of proteins:
a. Select Add Proteins to open the Add Proteins dialog.
b. In the Name field, enter a label for a detected protein or group of proteins.
c. In the Proteins field, enter a protein name or enter multiple names separated by commas. d. Select Add.
Notice that the label you entered for the protein or group of proteins is now selected.
4. To edit a protein or group of proteins:
TIP
To revert to using the default QC landmark proteins, select Abundance monitoring.
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Chapter 3 Analysis Results Analysis Metrics tab
a. Select its (Edit) button to open the Edit Proteins dialog.
b. Change the fields as needed.
c. Select Edit to save the changes.
5. To delete a protein or group of proteins:
a. Select its (Delete) button.
b. Select OK to confirm.
6. Select Continue to apply the settings.
PCA Analysis section
The PCA Analysis section clusters similar samples in a scatter plot. The x-axis plots principal component 1 (PC1) analysis scores and the y-axis plots principal component 2 (PC2) analysis scores. Each dot represents one sample.
• Select a dot under the x-axis to hide the corresponding sample.
• Hover over a dot to view the sample and plate names.
To customize this section for the selected analysis, see Change the PCA Analysis color scheme (below). Figure 12. Scatter plot showing clusters of similar samples
Change the PCA Analysis color scheme
You can temporarily change the color scheme of the PCA Analysis section (above). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Metrics tab. (See Open an analysis’s Analysis Metrics tab (page 44).)
2. In the PCA Analysis section, select an option from the Color By list:
– Condition — Applies the same color to all data points. The color represents sample quality.
– Sample Name — Applies a unique color to each sample.
– Plate Name — Applies the same color to all data points. The color represents the sample plate.
– Sample ID — Applies a unique color to each sample.
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Chapter 3 Analysis Results Analysis Metrics tab
3. Set colors as you prefer.
a. Select a label box next to or below the Color By list. For example, if you selected Sample ID
above, you can adjust the color for each sample.
b. Use the color picker to select a color. (See Set color preferences in PAS graphs (page 14).)
c. Repeat for other label boxes.
Peptide Counts Distribution and Protein Group Counts Distribution sections
The Peptide Counts Distribution and Protein Group Counts Distribution sections show the peptide and protein counts for the five nanoparticles as box plots. A table below each plot shows the analysis name, mean value, and CV percentage for each nanoparticle. Each box plot and table represent one plate.
• Hover over a dot to view the peptide or protein count, file, and sample name.
• Hover over a box to view the quantile for the nanoparticle.
Figure 13. Box plots showing peptide counts distribution
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Chapter 3 Analysis Results Analysis Metrics tab
Figure 14. Box plots showing protein group counts distribution
Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles sections
The Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles sections offer two charts:
• Protein Group Counts — Shows the sample protein group counts identified by each nanoparticle. Each
dot represents a sample. The x-axis plots samples and the y-axis plots the number of peptides.
• Peptide Counts — Shows the sample peptide counts identified by each nanoparticle. Each dot represents a sample. The x-axis plots samples and the y-axis plots the number of peptides.
To use these charts:
• Hover over a dot to view the well, nanoparticle that occupies the well, and the peptide count.
• Select a dot under the x-axis to remove the corresponding well from the plot.
To customize this section for the selected analysis, see Set Protein Group Counts of Nanoparticles and Peptide
Counts of Nanoparticles preferences (next page).
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Chapter 3 Analysis Results Analysis Metrics tab
Figure 15. Scatter plot showing protein group counts of nanoparticles
Figure 16. Scatter plot showing peptide counts of nanoparticles
Set Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles preferences
You can temporarily customize the appearance of the Protein Group Counts of Nanoparticles and Peptide Counts of Nanoparticles sections (previous page). The next time you view the section, it will have reverted to its default view.
1. Open the Analysis Metrics tab. (See Open an analysis’s Analysis Metrics tab (page 44).)
2. In the Protein Group Counts of Nanoparticles or Peptide Counts of Nanoparticles section, select
(Settings) to open the Preferences dialog.
3. Adjust the settings as you prefer.
– Y Axis Range — Select the range for the y-axis.
. Min is 0 and Max Data Dependent — The minimum value is set at 0 and the maximum value
depends on data.
. Min and Max Data Dependent — Both the minimum and maximum values depend on data.
. User Defined — Enter the minimum and maximum values.
4. Select Save.
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Chapter 3 Analysis Results Analysis Metrics tab
Hierarchical Clustering section
The Hierarchical Clustering section shows a cluster analysis based on agglomerative nesting, which groups samples in clusters based on similarity. Each sample starts a single cluster. Pairs of clusters are then successively merged until all clusters are merged into a dendrogram.
Figure 17. Dendrogram successively grouping similar samples
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Chapter 3 Analysis Results QC Charts tab
QC Charts tab
An analysis’s QC Charts tab (on the Analyses page) shows assay control data for an analysis. Each chart plots one metric for one assay control category. Charts are organized in a grid, with the same metric across each row and the same control type down each column. The x-axis is labeled with the date of analysis and the y-axis depends on the metric.
• Select a status icon (e.g., ) in the summary table above the control charts to jump to the corresponding control chart.
• Hover over a dot on a control chart to view general information about the control, such as well and plate.
Toolbar items
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.

• •
• • •
• •

— By default, all controls are included. Select another option to filter by a specific control type.
– Process Control — Results for the process controls only.
– Digestion Control — Results for the digestion controls only.
– MPE Control — Results for the MPE controls only.
– MS Peptide Control — Results for the mass spec controls only.
MS Instrument — The instruments listed vary depending on your organization. Select up to six instruments to aggregate their data.
Color By — (Available when only one MS instrumented is selected.) Select your preferred coloration for the graphs, e.g., Gradient.
Start Date — Enter or select the earliest date of data you want to see. End Date — Enter or select the latest date of data you want to see Control Limits — Select how you want control limits to be defined.
– –

Preinstalled — Use the preinstalled control limits.
User Defined — Define your own control limits. See Define and use user-defined control limits
(page 56).
Calculated — Calculate control limits from data within one or more date ranges, which you define with the Calculate button (see below).
Limits — Select to view the calculated control limit date ranges. From here, you can also delete a range. See Delete a calculated control limit date range (page 56).
Exclusion — Select to exclude an outlier or other data point from the control limit calculation. Selecting one data point (sample) in a plot excludes the corresponding sample from the other plots. A well containing the mass spec control has 10 reported QC metrics. All other control wells have 11 reported QC metrics. See Exclude a sample (page 56).
Calculate — Select to define a calculated control limit based on a range of dates. See Define and use calculated control limits (page 56).
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Chapter 3 Analysis Results QC Charts tab
• Annotate — Select to annotate all control charts for a specific date. See Annotate control charts (page 57).
• Reports — Select to generate a PDF report of control results, with specific criteria. See Generate a detailed PDF report of control results (page 58).
Figure 18. Results for controls
A Filters for viewing charts for all controls or a selected control type
B Toolbar with additional filters and functions
Open and filter an analysis’s QC Charts tab
C Summary of control data for the selected analysis time frame
D QC charts with metrics of each control
1. On the sidebar menu, select Analyses to open the Analyses page.
2. From the Status list, select Completed.
3. From the Controls/Samples list, select Samples included.
4. Select the checkbox of each applicable analysis whose QC charts you want to work with.
5. Select the QC Charts tab.
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Chapter 3 Analysis Results
QC Charts tab
The QC Charts tab (page 53) presents each control with metrics for assay and MS performance.
6. Under MS Instrument, select up to six instruments.
The tab aggregates data from the selected instruments and hides the Color By menu.
7. To filter the results for a specific control type, select an option:
– Process Control — Results for the process controls only.
– Digestion Control — Results for the digestion controls only.
– MPE Control — Results for the MPE controls only.
– MS Peptide Control — Results for the mass spec controls only.
8. To filter results for a specific time frame, enter the MS injection time frame in the Start Date and End Date fields.
Set QC Charts preferences
1. Open and filter the QC charts tab for an analysis. (See Open and filter an analysis’s QC Charts tab
(previous page).)
2. Select (Settings) to open the Preferences dialog.
3. Complete the fields as needed.
– Show Annotations — Select to show or hide annotation. See Annotate control charts (page 57).
– Show Historical Data — Select to show or hide historical data. By default, each control chart shows values from historical data. Although independent of the selected analyses, these data points are sourced from previous analyses that exist in the user group.
– Show Variables — Select the checkbox of each variable of interest, e.g., Protein Group Count, Peak Width (seconds). Clear the checkbox of any you’re not interested in.
– Process Variables Y Axis Range — Select the range for the y-axis for processed variables.
. Min and Max Data Dependent — Both the minimum and maximum values depend on data.
. Min is 0 and Max Data Dependent — The minimum value is set at 0 and the maximum value depends on data.
. User Defined — Enter the minimum and maximum values.
4. Select Save.
Manage user-defined and calculated control limits
Depending on the MS injection time frame, filtering results on the QC Charts tab by time frame shows a summary that presents each control with metrics for assay and MS performance. Each metric is color-coded to indicate whether it is within the control limits (teal) or outside the control limits (orange).
Control limits help determine whether results are expected. The mean provides a historical average, while the upper and lower control limits indicate normal variation. PAS includes default control limits calculated using two standard deviations above and below the mean. Calculated control limits are generated from user data.
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Chapter 3 Analysis Results QC Charts tab
Define and use user-defined control limits
1. On the Controls section’s toolbar, select the Control Limits list and select User Defined to open the Control Limits dialog.
2. Along the top of the dialog, select the tab of the control whose limits you want to define, e.g., MPE Control. Use the scroll arrows to view all tabs.
3. For each control limit, enter a value.
– Mean — The value to serve as the historical mean.
– UCL — The value to serve as the upper control limit.
– LCL — The value to serve as the lower control limit.
4. Select Save.
Define and use calculated control limits
1. On the Controls section’s toolbar, select Calculate to open the Calculate Control Limits dialog.
2. In the Start Date and End Date fields, enter or select the applicable dates.
3. Select Save.
A teal background appears on the plots, indicating that data are shown with modified control limits.
4. On the toolbar, select the Control Limits list and select Calculated to use the calculated control limits.
Delete a calculated control limit date range
1. On the Controls section’s toolbar, select Limits to open the Calculate Control Limits Range dialog.
2. Find the date range you want to delete and select its (Delete) button.
3. Select Yes to confirm.
4. Select Save.
Exclude a sample
Exclude an outlier or other data point from the control limit calculation. Selecting one data point (sample) in a plot excludes the corresponding sample from the other plots. A well containing the mass spec control has 10 reported QC metrics. All other control wells have 11 reported QC metrics.
1. Select Exclusion to open the Control Limit Exclusion dialog and display a list of samples that are being excluded.
2. Find the data point (sample) you want to remove and select its (Delete) button.
3. Select Yes to confirm.
4. Select Close.
NOTE
The new control limit date range has been added to the Calculate Control Limits Range dialog, which you can open with the Limits button.
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Chapter 3 Analysis Results QC Charts tab
Annotate control charts
You can add an annotation that will be applied to all control charts for a specific date. An annotation is indicated by a dot above a control chart with the full annotation below the chart. Select an annotation dot to view its annotation type, date, and accompanying message.
Add an annotation
1. Open and filter the QC charts tab for an analysis. (See Open and filter an analysis’s QC Charts tab (page 54).)
2. Select Annotate to open the Annotate dialog.
3. Complete the fields.
– Annotation Type — Do either of the following:
. To select an existing annotation type, select it from the list.
. To add a new annotation type, select Add Annotation Type, enter the annotation, and select Add.
– Date — Enter or select the date the event occurred.
– Message — Enter more information about the annotation.
4. Select Save.
Edit an annotation
1. Select the annotation dot for the annotation you want to edit.
2. In the annotation pop-up, select (Edit) to open the Annotate dialog.
3. Edit the annotation as needed.
4. Select Save.
Delete an annotation
1. Select the annotation dot for the annotation you want to delete.
2. In the annotation pop-up, select (Delete).
3. Select OK to confirm.
Generate reports of control results
Summarize and output control results in a .csv file or generate a more detailed report as a .pdf file. The summary lists each QC metric with the control, well, plate, value, and result. The report summarizes results and shows a table for each control. Each table includes the well and plate and lists values for each QC metric with optional notes.
Download summarized control results
1. Open and filter the QC charts tab for an analysis. (See Open and filter an analysis’s QC Charts tab (page 54).)
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Chapter 3 Analysis Results QC Charts tab
2. In the summary table above the control charts, select (Download CSV) to open the Download CSV dialog.
3. Select the checkbox of each field to add to the summary:
– File name — The full name of the MS data file, including extension.
– Assay instrument name — The name of the liquid handler that prepared the assay.
– Mass spec instrument name — The name of the MS instrument that analyzed the assay output.
– Injection time — The month and day of MS injection.
– Gradient — The duration of the LC gradient.
4. Select a format:
– One line per metric — Organizes the summary by metric.
– One line per control — Organizes the summary by control.
5. Select Download to generate the summary.
Generate a detailed PDF report of control results
1. Open and filter the QC charts tab for an analysis. (See Open and filter an analysis’s QC Charts tab (page 54).)
2. Select Reports to open the Controls Report dialog.
3. Complete the fields.
– Assay Equipment ID — Select the name of the liquid handler used to prepare the assay.
– Mass Spec ID — Select the name of the MS instrument that analyzed the assay output.
– Report By — (Read-only) Shows your username.
– Report Date — (Read-only) Shows the current date and time.
4. Select Create to generate the report.
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Chapter 3 Analysis Results Analysis Output Files tab
Analysis Output Files tab
An analysis’s Analysis Output Files tab (on the Analyses page) lists all outputs of the search engine results for the analysis. You can download an output file simply by selecting it.
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Chapter 4
Analysis Interpretation
Describes techniques for interpreting analysis results, specifically for group analyses, performed from the Group Analysis tab of the Analyses page.

Chapter 4 Analysis Interpretation
Open an analysis’s Group Analysis tab
Open an analysis’s Group Analysis tab
1. On the sidebar menu, select Analyses to open the Analyses page.
2. From the Status list, select Completed.
3. Select an analysis to open its analysis results.
4. Select the Group Analysis tab. (See Group Analysis tab (page 66).)
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Chapter 4 Analysis Interpretation Export raw data to a file
Export raw data to a file
Prior to doing a group analysis, you can export raw data to a .csv file.
1. Open the Group Analysis tab. (See Open an analysis’s Group Analysis tab (previous page).)
2. Select Export.
3. Navigate to the location on your computer where you want to save the file and select Save.
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Chapter 4 Analysis Interpretation View a raw protein group data heatmap
View a raw protein group data heatmap
Prior to doing a group analysis, you can visualize a heatmap of raw protein group intensity.
1. Open the Group Analysis tab. (See Open an analysis’s Group Analysis tab (page 61).) 2. Select Heatmap.
PAS prepares the data and then displays the heatmap.
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Chapter 4 Analysis Interpretation Set up and start a group analysis
Set up and start a group analysis
Follow these steps to prepare to conduct a group analysis in which you visualize differences in proteins detected between groups.
To begin this workflow:
1. Open the Group Analysis tab. (See Open an analysis’s Group Analysis tab (page 61).)
2. Select Setup Group Analysis to open the Setup Group Analysis dialog.
Continue to the next section.
Specify the quantitation level and grouping of samples
In the Feature and Grouping section, you specify the parameters for the differential expression analysis between groups of samples.
1. For Feature, select the quantitation level, either Protein or Peptide.
2. For Group By, select the category by which you want to group samples, e.g., by a condition or custom
field. The options vary based on the metadata imported from the sample description file.
3. Select Next to advance.
Filter out (exclude) samples and groups
In the Filter Samples and Group section, you specify the individual samples or whole groups of samples to be filtered out of (excluded from) the final comparison.
1. (Optional) From Select Sample, select one or more samples.
– If you change your mind about an excluded sample, select its (Delete) button.
2. (Optional) From Select Groups, select one or more groups of samples.
– If you change your mind about an excluded group, select its (Delete) button.
3. Select Next to advance.
Filter out (exclude) proteins or peptides
In the Filter Peptides / Proteins section, you specify measurement completeness thresholds for the final comparison.
1. Complete the fields.
NOTE
PAS will use whichever minimum (percentage or specific value) yields the larger number of samples.
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Chapter 4 Analysis Interpretation Set up and start a group analysis
– Minimum % of valid values in at least one group — Enter the minimum percentage of samples to consider. For example, if there are 24 samples and you enter 50, a minimum of 12 samples will be considered. The default is 0.
– Minimum number of valid values in at least one group — Enter the exact minimum number of samples to consider. The default is 2.
– Remove peptides / proteins with complete missing values in at least one group — Select to exclude peptides / proteins for which data is entirely missing (i.e., all table cells that show -).
– Remove peptides / proteins with missing values — Select to exclude peptides / proteins with one or more missing values (i.e., some table cells that show -).
2. Select Next to advance.
Normalize values and impute sparse or missing values
In the Normalization and Imputation section, you specify the processes by which raw measurement values are normalized and sparse and missing values are handled.
1. For Normalization, select either:
– Median — Raw MS intensity values are normalized on a run-by-run basis. This will account for
potential measurement bias and make samples more comparable.
– None — No normalization of raw measurements will occur.
2. For Imputation, select either:
– Minimal Probability — Substitute missing values with random values from a normal distribution using a mean that is down-shifted from the sample mean and a standard deviation (SD) that is a fraction of the SD of the sample distribution.
– None — No imputation of raw measurements will occur.
3. Select Next to advance.
Select the statistical test and the groups to compare
In the Statistical Test and Group Comparison section, you select the statistical test to use for comparison analysis and then select the groups of samples you want to compare.
1. For Statistical Test, select the appropriate test to use for comparison analysis.
– T Test — A parametric test. Select this if you previously elected to normalize data.
– Wilcoxon — A non-parametric text rank-based test. Select this if you previously elected not to normalize data.
2. Under Groups for Comparison, select the checkbox of each set of groups you want to compare. The groups offered vary, based on selections you made earlier in the setup workflow.
3. Select Start.
The group analysis begins immediately. When it is finished, the analysis results are shown on the Group Analysis tab, organized into sections, with the Volcano section being shown. To explore all the sections, begin at Group Analysis tab (next page).
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Chapter 4 Analysis Interpretation Group Analysis tab
Group Analysis tab
An analysis’s Group Analysis tab (on the Analyses page) shows the analysis and results from comparing two user-defined groups, organized into sections. You can visualize differences in proteins detected between the groups and explore initial biological insights into the data.
Toolbar items
• Before you run a group analysis, the toolbar includes:

– – –
– –
Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item (page 13).
Feature — Select Protein or Peptide to filter the Raw Data table.
Group By — Select the categorical grouping by which you want to group raw data.
Heatmap — (Not applicable to peptides.) Select to visualize a heatmap of raw protein group data. See View a raw protein group data heatmap (page 63)
Export — Select to export raw data to a .csv file. See Export raw data to a file (page 62).
Setup Group Analysis — Select to set up groups for and start a comparative analysis. See Set
up and start a group analysis (page 64).
• After you run a group analysis, the toolbar includes these additional items:

– – –
– –



Raw Data / Results — Use to switch back and forth between the raw data and group analysis results.
Significant Proteins — Select to show only significant proteins.
Volcano Plot — Select to view the Volcano section (page 69).
Coverage — (Available when at least two proteins are selected.) Select to view the Coverage section (page 70).
Clustered Heatmap — Select to view the Clustered Heatmap section (page 68).
PPI Network — (Available only for significant proteins.) — Select to view the Filtered PPI
Network section (page 71).
Enrichment — (Available only for significant proteins.) — Select to view the Enrichment section
(page 72).
Box Plots — (Available only for significant proteins.) — Select to view the Box Plots section
(page 73).
Preferences — Select to set threshold preferences. e.g., High Regulation Threshold.
Raw Data section
The Raw Data section shows a table consisting of protein groups (rows) identified across the analyzed samples (columns) and their corresponding intensity levels (values). Samples for which a protein group was detected show a numerical value. However, samples for which a protein group was not detected show a hyphen – character.
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Chapter 4 Analysis Interpretation Group Analysis tab
• Search for the protein (protein group) to extract intensity values across samples.
• Select the protein to visualize the distribution of abundances between samples corresponding to each
group as an Intensity Plot box plot.
• Select the Heatmap button to visualize a heatmap of raw protein group data.
Figure 19. Raw Data table listing proteins and Intensity Plot for the selected protein
Figure 20. Raw data table listing proteins and heatmap for all proteins
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Chapter 4 Analysis Interpretation Group Analysis tab
Clustered Heatmap section
After doing a group analysis, you can view the Clustered Heatmap section.
Here you can visualize protein abundances across samples, with both proteins (rows) and samples (columns)
clustered based on agglomerative nesting. Cell colors range from blue (lowly abundant) to red (highly abundant).
• Use the + and – buttons to zoom in and out of the graph.
• Hover over a cell to reveal the protein name, sample name, and abundance.
• Select (“hamburger menu”) to download the graph as .svg or .png.
Figure 21. Clustered heatmap graph
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Chapter 4 Analysis Interpretation Group Analysis tab
Volcano section
After doing a group analysis, you can view the Volcano section.
Here you can visualize a scatter plot showing the statistical significance (p-value) in abundance differences between your compared groups versus the magnitude of the change (Fold Change). Highlighted in the teal quadrants are proteins with large fold changes (default: ±2) and statistically significant (default: p < 0.05). Data displayed in the plot are shown in detail in the table on the left of the plot.
• Each point in the plot represents a protein. Hover over each point to display the protein group, fold change, and p-value.
• Clear the Significant Proteins checkbox in the Group Analysis section’s toolbar to display both significant and non-significant proteins.
• Select this section’s (Settings) button to highlight a protein of interest.
• Select (“hamburger menu”) to download the graph as .svg or .png.
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Chapter 4 Analysis Interpretation Group Analysis tab
Figure 22. Volcano graph
Coverage section
After doing a group analysis, you can view the Coverage section.
Here you can visualize the amino acid sequence of your selected protein and the regions where measured
peptides map. You must select at least one protein in the list to the left of this section. Coverage is represented as percent (%) of sequence observed by measured peptides.
• In cases where a PTM is detected for your selected protein, use the Coverage list to change to PTM to view where the PTM occurs.
• Select (Expanded View) to expand the section so you can see data more easily, without its wrapping
• Select (“hamburger menu”) to download the graph as .svg or .png.
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Chapter 4 Analysis Interpretation Group Analysis tab
Figure 23. Coverage graph
Filtered PPI Network section
After doing a group analysis and with the Significant Proteins checkbox selected, you can view the Filtered PPI Network section.
Here you can visualize a network plot showing protein-protein interactions between proteins with significantly different abundances between groups compared.
• Select this section’s (Settings) button to adjust the confidence of the Minimum Interaction Score.
• Nodes in the graph are selectable to view protein description and can be moved around.
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Chapter 4 Analysis Interpretation Group Analysis tab
Figure 24. Filtered PPI Network graph
Enrichment section
After doing a group analysis and with the Significant Proteins checkbox selected, you can view the Enrichment section.
Here you can functionally characterize proteins showing abundance difference between groups compared by performing gene ontology (GO) enrichment.
• Use the list to switch between GO categories: Molecular Function, Biological Process, and Cellular Compartment.
• Select this section’s Chart Settings button to set the cutoff (adjusted p-value upper limit).
• Display the GO term enrichment as either:
– Dot Plot — To “condense” similar terms by family (i.e., condense all children from each superfamily), select Summarize Terms.
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Chapter 4 Analysis Interpretation
Group Analysis tab

.
. .
Ontology Plot (hierarchical tree)
Hover over a box to view its GO information.
Use the mouse wheel to zoom into and out of the plot.
Drag the plot to reposition it so that you can examine different areas.
Figure 25. Enrichment plot, shown as an ontology plot (hierarchical tree)
Box Plots section
After doing a group analysis and with the Significant Proteins checkbox selected, you can view the Box Plots section.
Here you can visualize the intensity differences between groups of significantly different proteins.
• Select this section’s (Settings) button to set layout preferences for the charts.
• Hover over a dot to view a sample’s count and name.
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Chapter 4 Analysis Interpretation Group Analysis tab
Figure 26. Box plots
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Chapter 5
Data Management
Covers the components of and how to work with PAS’s main pages.

Chapter 5 Data Management Plates and samples
Plates and samples
A plate in PAS represents a Peptide Collection Plate, which is the output of the Proteograph Assay method analyzed with MS. A plate contains the samples, controls, and nanoparticles from a method run with the corresponding metadata.
Plates page
Use the Plates page to manage plates and sample information and to upload custom files. • To open this page, select Plates on the sidebar menu.
Toolbar items
• Add Plate — Select to add a plate to PAS when setting up an analysis. See Setup workflow: Add a plate (page 25).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item (page 13).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table columns (page 12).
Table columns
• Name — The name of the plate.
• Plate ID — The unique identifier of the plate.
• Description — The description of the plate.
• Notes — Additional information about the plate.
• Created By — The user who created the plate.
• Created Time — The date and time the plate was created.
• Last Modified By — The user who last modified the plate.
• Last Modified Time — The date and time the plate was last modified.
• ID — The unique, internal identifier of the plate.
• (Add Sample) — Select to add samples to the selected plate. See Add samples to an existing plate (page 79).
• (Edit) — Select to edit the selected plate. See Edit a plate (next page). Other page sections
• Plate Samples — Shows a table of samples associated with the plate selected in the Plates section. For detailed information about this section, see Plate Samples section (page 78).
• Plate Grid — Shows a grid or table of wells associated with one or more samples selected in the Plate Samples section. For detailed information about this section, see Plate Grid section (page 81).
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
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Chapter 5 Data Management Plates and samples
Review a plate
1. On the sidebar menu, select Plates to open the Plates page.
2. Select a plate to review.
The Plate Samples table appears, listing the samples in the selected plate.
3. (Optional) Adjust the table view as needed:
– To adjust the number of visible table rows, scroll to the bottom of the table and select the number of items per page.
– To sort a table column, select the column heading to sort in descending order. To sort in ascending order, reselect the column.
– To filter samples, enter a keyword or term in the Search field.
4. Select samples for review:
– To review all samples, select the checkbox in the column heading.
– To review selected samples, select each sample’s checkbox.
The Plate Grid appears, showing the plate with yellow wells indicating the selected samples.
5. Review sample details:
– To individually review sample details, select a yellow well.
– To simultaneously review details for all samples, select Table View.
– To modify sample details, see Edit or delete samples in wells (page 81).
Edit a plate
1. On the sidebar menu, select Plates to open the Plates page.
2. Find the plate you want to edit and select its (Edit) button to open the Edit Plate dialog.
3. Edit the fields as needed.
– Plate ID — Enter a unique identifier for the plate.
– Plate Name — Enter a descriptive name for the plate.
– Description — (Optional) Enter a description of the plate.
– Notes — (Optional) Enter additional information about the plate.
4. Select Confirm to save.
Delete a plate
1. On the sidebar menu, select Plates to open the Plates page.
2. Find the plate you want to delete and select its (Delete) button.
3. Select OK to confirm.
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Chapter 5 Data Management Plates and samples
Plate Samples section
The Plate Samples section is part of the Plates page (page 76).
• To open it, select Plates on the sidebar menu and then select a plate. You many need to scroll down to see the Plates Samples section.
Toolbar items
• Link to Sample Description File — Select to link a sample description file to the selected plate. See Add sample descriptions (page 80).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item (page 13).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table columns (page 12).
Table columns
• Name — The descriptive name of a sample.
• Sample/Control ID — The unique identifier of a sample or control.
• Well Location — The location of a sample or control in the selected plate.
• Type — The type of sample: Plasma or Peptide.
• Species — The species a sample was collected from: Human or Mouse.
• Sample Collection Date —The date the sample was collected.
• Sample Receipt Date — The date your laboratory received the sample.
• Condition — The categorical group the sample belongs to.
• Biological Replicate — The biological replicate number.
• Technical Replicate — The technical replicate number.
• Description — The description of the sample.
• Notes — Additional information about the sample.
• Created By — The user who created the sample.
• Created Time — The date and time of the sample was created.
• Last Modified By — The user who last modified the sample.
• Last Modified Time — The date and time the sample was last modified.
• ID — The unique, internal identifier of the sample.
• Plate ID — The unique identifier of the plate.
• Plate Name — The descriptive name of the plate.
• (Edit) — Select to edit information about the selected sample. See Edit sample information (page 80).
• (Delete) — Select to delete the selected sample. See Delete a sample from a plate (page 81).
TIP
You can add custom columns to this table. See Add custom columns (page 12).
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Chapter 5 Data Management Plates and samples
Add samples to an existing plate
Adding samples to an existing plate follows a similar workflow to the add-a-plate workflow of analysis setup (described in Setup workflow: Add a plate (page 25)). The difference is that in the add-a-plate workflow, you add a new plate and its samples to PAS, whereas you can also add samples to an existing plate, as described below.
1. On the sidebar menu, select Plates to open the Plates page.
2. Find the plate to which you want to add sample and select its (Add Sample) button to open the Add
Sample dialog.
3. In the MSDATA Files section, you add one or more MS data files.
a. Select the MS data files.
– To add a single file, select Files to open the Add Files dialog.
– To add multiple files, select Folder to open the Add Folder dialog.
b. Either drag the file or folder into the drag-and-drop area or use Browse to navigate to and select
it.
c. Select Add.
d. Review the selected files.
– To remove a file, select (Delete).
– To remove all files, select Clear.
e. Select Next to advance.
4. In the Plate Map File section, you add a plate map file, which specifies the locations of samples.
a. If you don’t have a plate map file, create one before continuing.
A. Select the on-screen link from which you can download an example plate map file (.csv).
B. Open the file and edit it as needed.
The MS file name, Sample ID, and Plate ID columns are required. (See Plate map file format (page 15) for detailed descriptions of the columns in the file.)
C. Save as a .csv file.
b. Select Add File or Add to open the Add File dialog.
c. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
d. Select Add.
e. Select Next to advance.
5. In the Plate ID and Name section, you link the MS data files to an existing plate.
a. Select Use Existing Plate, and then select the applicable plate.
b. Select Next to advance.
6. (Optional) In the Sample Description File section, you upload metadata for each sample in the plate.
NOTE
Supported file formats are .raw, wiff, or .wiff.scan. Supported folders are RAW and D.
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NOTE
This part of the workflow is optional. To skip it, select Next to advance.
a. Select Add or Add File to open the Add Files dialog.
b. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
c. Select Add.
d. Select Next to advance.
7. In the Add to Project section, you add the samples to a new or existing project.
a. Create or select a project:
– To create a new project, select New Project, enter a project name, and select Add.
– To use an existing project, select it from the Select Project list.
b. Select or clear the applicable checkboxes. (To defer analysis, clear both checkboxes.)
– Analyze samples after addition — Select to analyze samples.
– Analyze controls after addition — Select to analyze controls.
c. Select the MS method:
– DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.
– DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
d. From the Analysis Protocol list (which shows only protocols compatible with the selected MS method), select a protocol.
e. Select Add Plate, and then select Close.
– If you had selected either or both Analyze… checkboxes earlier, the analysis starts
immediately.
– If you deferred analysis, you must start it manually. See Start the analysis (page 27).
Add sample descriptions
1. On the sidebar menu, select Plates to open the Plates page.
2. In the Plates table, select a plate to add sample descriptions to.
3. On the Plate Samples section’s toolbar, select Link to Sample Descriptions File to open the Upload File dialog.
4. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
5. Select Upload.
The information from the uploaded file appears in the Plate Samples section of the Plates page.
Edit sample information
1. On the sidebar menu, select Plates to open the Plates page.
2. Select the plate for which you want to edit information about a sample.
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Plates and samples
3. In the Plate Samples table, find the sample you want to edit and select its Edit window.
4. Complete the fields as needed.
5. Select Confirm to save.
Delete a sample from a plate
(Edit) button to open the
1. On the sidebar menu, select Plates to open the Plates page.
2. Select the plate from which you want to delete a sample.
3. In the Plate Samples table, find the sample you want to delete and select its (Delete) button.
4. Select OK to confirm.
Plate Grid section
The Plate Grid section of the Plates page shows the selected plate with yellow wells indicating the samples selected in the Plate Samples list.
The section offers two views of the same information. Grid View facilitates editing and deleting samples one well at a time, while Table View offers a more efficient means to work with samples in multiple wells. For detailed instructions, see Edit or delete samples in wells (below).
If you have created a custom .csv, .tsv, .xls, or .xlsx file containing sample information, you can upload it to the Plates page from the Plate Grid section. See Upload a custom file containing sample information (next page).
Edit or delete samples in wells
The Plate Grid section of the Plates page offers two views for editing samples in and deleting samples from wells. Grid View facilitates editing and deleting samples one well at a time, while Table View offers a more efficient means to work with samples in multiple wells.
1. On the sidebar menu, select Plates to open the Plates page.
2. Select the plate whose samples you want to edit or delete.
3. In the Plate Samples table, select the checkbox of each sample you want to work with.
The Plate Grid appears below the Plate Samples table and shows the selected samples as yellow wells in a 96-well plate.
4. Edit or delete samples as described below.
Grid view
1. Select Grid View if it is not already selected.
2. To edit a sample in a well:
a. Select a yellow well to open its details and then select its (Edit) button.
b. Edit values in the editable fields. PAS saves each change as you work.
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c. When finished editing, select the (Edit) button again to save all the changes. 3. To delete a sample from a well :
a. b.
Table view
Select a yellow well to open its details and then select its (Delete) button. Select OK to confirm.
Table View.
– To edit an individual cell, enter a value, and then press Enter.
1. Select
2. To edit samples in a well:
– To apply the same value to all cells in a column, select the column heading’s enter a value, and then select Apply.
(Update) button,
– To copy and paste a row, scroll all the way to the right and select (Copy). Edit the copied row as
needed and then select (Save Copy).
3. To delete a sample from a well, select the well’s (Delete) button. Select OK to confirm.
Upload a custom file containing sample information
You can create a custom .csv, .tsv, .xls, or .xlsx file containing sample information and upload it from the Plates page. To create the file, match the columns in the file to the columns in the table view.
1. On the sidebar menu, select Plates to open the Plates page.
2. Select the applicable plate.
3. In the Plate Samples table, select the checkbox of at least one sample to open the Plate Grid sections.
4. Select (Upload File) to open the Upload File dialog.
5. Either drag the file into the drag-and-drop area or use Browse to navigate to and select it.
6. Select Upload.
PAS populates the plate grid with imported sample information.
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Chapter 5 Data Management Projects
Projects
When you set up an analysis, PAS creates a corresponding project and adds it to the Projects page. The project lists all samples in an analysis with sample information. On the Projects page, you can add samples to the analysis and then start the analysis.
Projects page
Use the Projects page to manage projects, to manage the samples associated with a project, and to view the MS data files associated with a specific sample.
• To open this page, select Projects on the sidebar menu.
Toolbar items
• Add Project — Select to add a new project. See Add a project (next page).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item
(page 13).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table
columns (page 12).
Table columns
• Tenant ID — The user identification.
• Name — The name of the project.
• Description — The description of the project.
• Notes — Additional information about the project.
• Created By — The user who created the project.
• Created Date — The date and time of project was created.
• Last Modified By — The user who last modified the project.
• Last Modified Date — The date and time the project was last modified.
• ID — The unique, internal identifier of the project.
• (Edit) — Select to edit the selected project’s name, description, and/or notes.
• (Delete) — Select to delete the selected project (one that you originally added). See Delete a project
(next page). You cannot delete someone else’s project (unless you are an Admin). Other page sections
• Sample List — Shows a table of samples associated with the project selected in the Projects section. For detailed information about this section, see Sample List section (next page).
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
TIP
You can add custom columns to this table. See Add custom columns (page 12).
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• MS Data files — Shows a read-only table of MS data files associated with the sample selected in the Samples List section. You can show or hide columns and can search for a specific data file.
Add a project
1. On the sidebar menu, select Projects to open the Projects page.
2. Select Add Project to open the Create Project dialog.
3. Complete the fields.
– Project Name — Enter a unique name for the project.
– Select Plate — Select a plate to add to the project.
– Add — Select to add another plate to the project. Repeat as needed.
– Description — Enter a description of the project.
– Notes — Enter any additional information about the project.
4. Select Save.
Delete a project
You can delete any project that you originally created. You cannot delete someone else’s project unless you are an administrator.
1. On the sidebar menu, select Projects to open the Projects page.
2. Find the project you want to delete and select its (Delete) button.
3. Select Yes to confirm.
Sample List section
The Sample List section of the Projects page (previous page) shows a table of samples associated with the
selected project.
• To open it, select Projects on the sidebar menu and then select the project whose samples you want to manage.
Toolbar items
• Add Sample — Select to add samples to the project. See Add samples to a project (next page).
• Analyze — Select to select samples for analysis, as described in Setup workflow: Select samples or
controls for analysis (page 31).
• Analyze Controls — Select to select controls only for analysis. See Analyze controls only (page 32).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item (page 13).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table columns (page 12).
TIP
You can add custom columns to this table. See Add custom columns (page 12).
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Table columns
• Tenant ID — The user identification.
• Name — The descriptive name of a sample.
• Sample/Control ID — The unique identifier of a sample or control.
• Well Location — The location of a sample or control in the selected plate.
• Type — The type of sample: Plasma or Peptide.
• Species — The species a sample was collected from: Human or Mouse.
• Sample Collection Date —The date the sample was collected.
• Sample Receipt Date — The date your laboratory received the sample.
• Condition — The categorical group the sample belongs to.
• Biological Replicate — The biological replicate number.
• Technical Replicate — The technical replicate number.
• Plate Name — The descriptive name of the plate.
• Description — The description of the sample.
• Notes — Additional information about the sample.
• Created By — The user who created the sample.
• Created Date — The date and time of the sample was created.
• Last Modified By — The user who last modified the sample.
• Last Modified Date — The date and time a sample was last modified.
• ID — The unique, internal identifier of the sample.
Add samples to a project
1. On the sidebar menu, select Projects to open the Projects page.
2. Select a project to add samples to.
3. Above the Sample List table, select Add Sample to open the Add Sample dialog.
4. Complete the fields.
– Select Plate — Select the plate to add samples to.
– Select Sample — Select a sample to add.
– Add — Select to add another sample.
5. Select Save to add the selected samples.
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Analyses
When you set up an analysis, PAS adds the analysis to the Analyses page with general information about the analysis: the number of MS data files in the analysis, who last modified the analysis and when, and optional notes and descriptions. An icon to the left of the analysis name indicates the status. Selecting an icon opens the analysis log.
Analyses page
Use the Analyses page to manage analyses and to view and download analysis results and logs. • To open this page, select Analyses on the sidebar menu.
Toolbar items
• Project — Select the project whose analysis data you want to work with.
• Plate — Select the plate whose analysis data you want to work with.
• Controls/Samples — Select whether to show controls or samples on the list.
• Status — Select the status of analyses that you’re interested in, e.g., Completed.
• Refresh — Select to refresh the table.
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item
(page 13).
• (Menu) — Select to open a menu of options (e.g., Delete) to use when multiple analyses are selected.
See Delete one or more analyses (page 88).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table
columns (page 12).
Table columns
• — The status of an analysis: (Succeeded), (Failed).
• Name — The name of an analysis.
• Description — The description of the analysis.
• Notes — Additional information about the analysis.
• Protocol — The protocol used for the analysis.
• MS Data Files — The number of MS data files associated with the analysis.
• Analyzed By — The user who created the analysis.
• Analysis Start — The date and time the analysis started.
• Analysis End — The date and time the analysis ended.
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
TIP
You can add custom columns to this table. See Add custom columns (page 12).
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• • •
• •
Last Modified By — The user who last modified the analysis.
Last Modified Time — The date and time the analysis was last modified. ID — The unique, internal identifier of the analysis.
(Edit) — Select to edit the selected analysis. See Edit an analysis (below).
(Delete) — Select to delete the selected analysis. See Delete one or more analyses (next page).
Download an analysis log
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Find the analysis whose log you want to download and select the status icon (e.g., (Succeeded)) that
precedes its name.
The Analysis Log dialog opens, listing all analysis events from oldest to newest.
3. Select (Download Log).
4. Depending on your browser or browser preferences, the file may download immediately, or you may be
prompted where to save the file. Follow any on-screen prompts.
Download an analysis’s protein groups and peptides results
You can download results for protein groups and peptides for a selected analysis. The results are organized into several files, each offering simplified data tables containing summarized results.
• Peptide_NP.tsv — Peptides, abundances, and other metadata across nanoparticles.
• Peptide_Panel.tsv — Peptides, abundances, and other metadata with nanoparticle values rolled up.
• Protein_Group_NP.tsv — Protein groups, abundances, and other metadata across nanoparticles.
• Protein_Group_Panel.tsv — Protein groups, abundances, and other metadata with nanoparticle values rolled up.
To download analysis results:
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Select the analysis whose results you want to download.
3. Select Protein Group / Peptide Results, located to the right of the of the analysis’s tabs.
4. Depending on your browser or browser preferences, the file may download immediately, or you may be prompted where to save the file. Follow any on-screen prompts.
Edit an analysis
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Find the analysis you want to edit and select its (Edit) button to open the Edit Analysis dialog.
3. Edit the fields as needed.
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– Analysis Name — Enter a name of the analysis.
– Description — (Optional) Enter a description of the analysis.
– Notes — (Optional) Enter additional information about the analysis.
4. Select Save.
Delete one or more analyses
To delete a single analysis:
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Find the analysis you want to delete and select its (Delete) button.
3. Select OK to confirm.
To delete multiple analyses:
1. On the sidebar menu, select Analyses to open the Analyses page.
2. Select the checkbox of each analysis you want to delete.
3. Select (Menu) and then select Delete.
4. Select OK to confirm.
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MS data files
When you upload MS data files during analysis setup, PAS creates a folder to contain the files. From the Data Files page, you can customize any folder and manually create folders.
Use the following filters to refine your view of the Data Files page.
• Start Date and End Date — Filter for folders and files created within a specified date range.
• Last Uploaded — Filter for folders and files uploaded within the last day, last five days, or last month. Data Files page
Use the Data Files page to create, move, and delete MS data files and folders and to download an application for automatic file updates.
• To open this page, select Data Files on the sidebar menu.
Toolbar items
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.

• •
• • • •
• •
Link to Plate — (Available when one or more files or folders are selected.) Select to link the selected files or folders to a plate when setting up an analysis. See Setup workflow: Link to a plate (page 28).
New — Select to add a new, empty folder.
Upload — Select to upload data files. See Upload MS data files (next page).
Refresh — Select to refresh the table.
Start Date — Set the earliest creation date for the files you want to view.
End Date — Set the latest creation date for the files you want to view.
Last Uploaded — Select a filter the list to show only those files created or uploaded within the last day (1D), last five days (5D), or last month (1M). To clear the active filter, select it again.
(Menu) — Select to move, rename, or delete the selected files or folders. See Move MS data files (next page), Rename MS data files or folders (next page), and Delete MS data files or folders (page 91).
Uploader — Select to download the Seer AutoUploader application with which you can automatically transfer new MS data files to PAS. You may find it a more convenient means of uploading a large set of
files rather than using the Upload button. See Download and install the Seer AutoUploader application (page 91).
Table columns
• <folders/files> — Initially shows the top level of folders into which data files are organized. Select a folder to view its contents. The column’s heading shows the breadcrumb (path) to the folder whose contents are listed. To return to another folder in the path, select its link in the breadcrumb. To return to
the top-level folders, select (Home).
• Filepath — Shows the location where a file or folder is stored.
• Date — Shows the date the file or folder was added to PAS.
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• •
• •
Time — Shows the time the file or folder was added to PAS. Size — Shows the disk size of the file or folder.
(Download) — Select to download the selected file.
(Delete) — Select to delete the selected file or folder. See Delete MS data files or folders (next page).
Create a folder
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Select New to open the Create Folder dialog.
3. Enter the name of the new folder.
4. Select Create.
Upload MS data files
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Select Upload to open the Add Raw MSDATA Files dialog.
3. Select the MS data files.
– To upload a single file, select Add Files to open the Add Files dialog.
– To upload multiple files, select Add Folder to open the Add Folder dialog.
4. Either drag the file or folder into the drag-and-drop area or use Browse to navigate to and select it.
5. Select Upload.
6. Review the uploaded files.
– To remove a file, select (Delete).
– To remove all files, select Clear.
Move MS data files
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Select the folder where the MS data files you want to move are stored.
3. Select the checkbox of each file you want to move.
4. Select (Menu) and then select Move.
5. Select a destination folder, and then select Move Here.
6. Select OK to confirm.
Rename MS data files or folders
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Navigate to the folder where the folder or file you want to rename is stored.
3. Select the checkbox of the folder or file you want to rename.
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4. Select (Menu) and then select Rename.
5. Enter a new name for the folder or file.
6. Select Save, and then select OK.
Delete MS data files or folders
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Navigate to the folder where the folder or file you want to delete is stored.
3. Find the folder or file you want to delete and select its (Delete) button.
4. Select OK to confirm.
Download and install the Seer AutoUploader application
The Seer AutoUploader is an application that runs on your MS computer to automatically upload new MS data files to your PAS account. You may find it a more convenient means of uploading a large set of files rather than
using the Upload button on the Data Files page.
1. On the sidebar menu, select Data Files to open the Data Files page.
2. Select
Uploader to open the Download AutoUploader dialog.
a. From Select file to download, select the version of the AutoUploader you want to download.
b. In the Save As window, navigate to the folder in which you want to save the installation package
and select Save.
c. Select Done.
3. In your computer’s file system, navigate to and double-click the installation package to launch it. Follow the prompts to install the software.
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Analysis protocols
Analysis protocols
An analysis protocol specifies search parameters for the MS database search engine.
• For DDA-based analyses, PAS uses the MaxQuant1 protocol.
• For DIA-based analyses, PAS uses either the EncyclopeDIA2 or DIA-NN3 protocol.
PAS includes several preinstalled analysis protocols, identified on the Protocols page (below) by the icon. You can also create custom protocols by copying an existing protocol or by uploading a protocol.
(star)
1Cox, Jürgen, and Matthias Mann, “MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification,” 26 Nature Biotechnology (November 2008): 1367–1372, https://doi.org/10.1038/nbt.1511.
2Searle, Brian C., Lindsay K. Pino, Jarrett D. Egertson, Ying S. Ting, Robert T. Lawrence, Brendan X. MacLean, Judit Villén, et al., “Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry,” 9 Nature Communications (December 2018): 5218, https://doi.org/10.1038/s41467-018-07454- w.
3Demichev, V., Messner, C.B., Vernardis, S.I. et al., “DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.” 17 Nat Methods (January 2020): 41–44, https://doi.org/10.1038/s41592- 019-0638-x.
Protocols page
Use the Protocols page to manage analysis protocols and to view analysis parameters. • To open this page, select Analysis Protocol on the sidebar menu.
Toolbar items
TIP
Use (Collapse) and (Expand) (where available) to selectively collapse and expand sections as you work.
• Copy — (Shown when a protocol is selected.) Select to copy a custom (user-defined) or preinstalled protocol. See Copy an analysis protocol (page 94).
• Upload — Select to upload a protocol. See Upload an analysis protocol (next page).
• Search — Use to filter the table or find a specific item. See Filter a table; search for a specific item
(page 13).
• Show/Hide — Select or clear checkboxes to show or hide table columns. See Show or hide table
columns (page 12).
Table columns
• Name — The name of the protocol.
• Type — Whether the associated MS method is DDA or DIA.
TIP
You can add custom columns to this table. See Add custom columns (page 12).
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• Species — Whether the analyzed sample is from a human or mouse.
• Version — The version of the protocol, useful if you want to keep track of different versions (updates) of
protocols.
• Description — The description of the protocol.
• Notes — Additional information about the protocol.
• Created By — The user who created the protocol.
• Created Time — The date and time the protocol was created.
• Parameters — The name of the file in which the search engine parameters are defined. To view the search engine parameters for a protocol, select its row. See View an analysis protocol’s search engine parameters (below).
• Preinstalled — Shows which protocols are preinstalled (indicated by (star)). You may copy but not delete preinstalled protocols.
• ID — The unique, internal identifier of the protocol.
• (Download) — Select to download a protocol. See Download an analysis protocol (next page).
• (Delete) — Select to delete selected protocol. See Delete an analysis protocol (next page). View an analysis protocol’s search engine parameters
1. On the sidebar menu, select Analysis Protocol to open the Protocols page.
2. Select the analysis protocol whose search engine parameters you want to view.
A panel opens to the right of the Protocols table to display the selected protocol’s parameters, which are read in from the protocol’s parameters file.
Upload an analysis protocol
1. On the sidebar menu, select Analysis Protocol to open the Protocols page.
2. Select Upload to open the Analysis Protocol dialog.
3. Complete the fields.
– Name — Enter a unique name for the protocol.
– Analysis Type— Select an MS method.
From the DDA list, select the MS method:
. DDA — Derives an MS/MS spectra from selection, isolation, and fragmentation of an individual
precursor ion.
. DIA — Derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
– Analysis Engine — Select an analysis engine, e.g., Max Quant.
For information about the analysis engines supported by PAS, see Analysis protocols (previous
page).
– Species — Select the species to analyze: Human or Mouse.
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– Description — Enter a description for the protocol.
– Notes — Enter any additional information about the protocol.
4. When ready to upload the protocol:
a. Select Upload to open the Upload File dialog.
b. Drag-and-drop the file or select Browse to navigate to and select the file.
c. Select Upload.
5. On the Analysis Protocol dialog, select Save.
Copy an analysis protocol
1. On the sidebar menu, select Analysis Protocol to open the Protocols page.
2. Select the protocol you want to copy and select Copy.
– For a DDA-based protocol, be sure to copy a DDA protocol.
– For a DIA-based protocol, be sure to copy a DIA protocol. The DDA and DIA fields cannot be modified in a copied protocol.
3. In the Edit Protocol dialog, edit fields for the new protocol.
4. Select Save.
Download an analysis protocol
1. On the sidebar menu, select Analysis Protocol to open the Protocols page.
2. Find the protocol you want to download and select its (Download) button.
3. On the Save As dialog, navigate to the folder where you want to save the protocol and select Save.
Delete an analysis protocol
1. On the sidebar menu, select Analysis Protocol to open the Protocols page.
2. Find the custom protocol you want to delete and select its (Delete) button.
3. Select OK to confirm.
NOTE
The search engine parameter fields vary, depending on the search engine being used, e.g., MaxQuant, Andromeda.
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Glossary A
Admin
Role that allows adding plates, creating projects, creating analysis protocols, viewing MS data files, viewing results files, and adding and deleting users.
analysis
A search for identification and annotation of LC-MS data.
Analysis Metrics
Tab that provides the QC metrics for an analysis result.
analysis protocol
The parameters for an MS database search in a .xml or .json file.
Analysis Summary
Tab that provides an overall view of analysis results.
annotation
A highlight or explanatory note added to a chart.
C
CO-RE
Compressed O-ring expansion.
consumables
Reagents and plasticware.
control limits
CV
D
data-dependent acquisition
MS method that derives an MS/MS spectra from selection, isolation, and fragmentation of an individual precursor ion.
data-independent acquisition
MS method that derives an MS/MS spectra from selection, isolation, and fragmentation of all precursor ions in a defined m/z range.
DDA
Data-dependent acquisition.
DIA
Digestion Control
A reference sample added before nanoparticle incubation.
distribution of detected proteins in plasma proteome
The dynamic range of proteins identified in each sample compared to a deep reported human plasma proteome index.
E
equipment
Reusable laboratory equipment.
H
hierarchical clustering
Cluster analysis based on agglomerative nesting, which groups samples in clusters based on similarity.
Parameters that help determine whether results are expected. The mean provides a historical average, and the upper and lower control limits indicate normal variation.
custom file
Optional sample information in a .csv, .tsv, .xls, or .xlsx file.
Coefficient of variation.
Data-independent acquisition.
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Glossary
IN
intensities
Protein and peptide intensities and the distribution of protein sequence coverage for each sample, including the coefficient of variation.
NCT
Nested conductive tips. Nanoparticle.
Nested tip rack.
P
PC1
PC2
Principal component 2.
PCA
Principal component analysis.
PCA analysis
Clusters of similar samples based on PC1 and PC scores.
PCC
Pearson correlation coefficient.
Pearson correlation coefficient
A measure of the linear correlation of data.
peptide counts
The number of peptides in each sample.
peptide counts distribution
Peptide counts for the five nanoparticles processed with the samples.
peptide counts of nanoparticles
Sample counts plotted by nanorparticle.
plate
The samples, controls, and nanoparticles from a Proteograph Assay method run.
L
NP NTR
lamppost protein concentration
The intensity of landmark proteins in each sample.
LC
LC-MS
Liquid chromatography-mass spectrometry.
LCL
Lower control limit.
M
Mass Spec Control
Reference peptides added before LC-MS analysis.
materials
Consumables and equipment.
MPE
Monitored multi-flow positive pressure evaporative extraction.
MPE Control
Reference peptides added before desalting cleanup. Mass spectrometry.
MS data file
The results of MS analysis for each sample or control in a plate in a .raw, .wiff, .wiff.scan file.
MS
Liquid chromatography.
Principal component 1.
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Glossary
plate map file
The location of each sample in a plate in a .csv file.
plate map grid
Metrics for each sample in the format of 96-well plates.
Plate Samples
Table listing all samples in a plate selected on the Plates page.
Plates
Table on the Plates page listing all plates in PAS.
Process Control
A reference sample added before nanoparticle incubation.
project
All samples in an analysis with sample information.
Projects
Table on the Projects page listing all projects in PAS.
protein group counts
The number of proteins in each sample.
protein group counts distribution
Protein group counts for the five nanoparticles processed with the samples.
protein group overlap sets
Protein group intersections, including intersection size and protein group counts.
Proteograh Analysis Suite
Seer software used to process, analyze, and visualize LC-MS data.
Proteograph
Descriptive product term.
Proteograph Assay Kit
The reagents and labware for preparing samples on the SP100.
Proteograph Instrument Control Software
Software onboard the SP100 used to operate the instrument.
Proteograph Product Suite
The bundle of Seer kit, instrument, and analysis software.
Protocols
Table on the Protocols page listing all analysis protocols in PAS.
Q
QC
QC charts
Charts presenting process control data for an analysis.
QC metrics
Metrics indicating how well an analysis performed.
R
report
A summary of control results in a .pdf file.
results file
The output of an analysis in .txt or .xml file format.
S
sample comparability
The degree of statistical correlation between samples based on the Pearson correlation coefficient or Jaccard index.
sample description file
Metadata for each sample in plate in a .csv file.
Sample list
List of all samples in a project selected on the Projects page.
Seer AutoUploader
An application that runs on the MS computer and automatically transfers new MS data files to PAS.
Quality control.
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Glossary
SP100 Automation Instrument
The Seer liquid handling instrument.
summary
A list of each QC metric with the control, well, plate, value, and result in a .csv file.
U
UCL
Upper control limit.
User
Role that allows adding plates, creating projects, creating analysis protocols, viewing MS data files, and viewing results files.
user group
A group of users that can access and view the plates, projects, and analyses of all other users in the group.
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Index
A
accounts 9, 14, 21 add
users 21 adding
custom table columns 12 adjusting tables 77 Analyses page 9, 34, 36, 86 analysis
DDA-based 92 DIA-based 92
metrics 44
performance 44
results 20, 37, 44 settings 20, 54
starting 26, 29, 79-80, 83 status 86
summaries 37 analysis interpretation 60 analysis logs 86-87 analysis metrics 34, 36 Analysis Metrics
Hierarchical Clustering section 52 Intensities section 44-45
Lamppost Proteins’ Concentration sec-
tion 46-47
PCA Analysis section 48
Peptide Counts Distribution section 49 Peptide Counts of Nanoparticles sec-
tion 50-51
Plate Map Grid section 46
Protein Group Counts Distribution sec- tion 49
Protein Group Counts of Nanoparticles section 50-51
Set Plate Map Grid section 45 analysis output files 59
Analysis Output Files tab 59 Analysis Protocol page 9, 92 analysis protocols 15, 19, 37, 79, 92
creating 92-94 defaults 19 parameters 92-94 selecting 31
analysis summary 34, 36 Analysis Summary
Distribution of Detected Proteins in Plasma Proteome section 39-
40
Peptide Counts section 38-39 Protein Group Counts section 37-38 Protein Group Overlap Sets
section 40-41
Sample Comparability section 42 Summary section 37
annotations 9, 39-40, 57 appearance, user interface 19 applications 91
assay controls 9
auto updater 91 B
bar graphs 40 box plots 44, 49 Box Plots 73 browsers 10
C
calculated control limits 55 calculations 39, 45, 55-56, 92 Chart Type preference 45 charts 44, 53
citations 39, 92
Clustered Heatmap 68 clusters 48, 52
coefficient of variation 44, 49 color codes 42, 55-56
Color Labels By preference 43 color scheme
PCA Analysis 48 columns
custom 16
descriptions 76, 83
plate map files 15
required 25, 28, 79 sample description files 16 showing and hiding 46 sorting 77
common proteins 37 comparing samples 52 compatible browsers 10 contact information, Seer 102 control charts 53, 55, 57 control software 15
controls
analyzing 27, 30-31 information 53 metrics 55, 57-58 results 53, 55, 57-58 types 15, 18, 53-54
Coverage 70
creating folders 90
creating projects 26, 29, 79-80, 84 cumulative protein groups 37 custom analysis protocols 92-94 custom columns 16
custom table columns 12 customer support 102
D
dark theme 19 data
distribution 44-45 hiding 55 reanalyzing 24, 31
Data Files page 9, 28, 89 defalt control limits 55 delete
users 22
deleting annotations 57 deleting folders 91 dendrograms 52
density 44
density plots 44-45
detected proteins 37, 39, 47 differences in proteins between
groups 66 digestion controls 18, 54
directories 28, 83, 89
disable authenticator app security 20 Display Percentage preference 41 Display Top N Intersection preference 41 Display Type preference 46
Distribution of Detected Proteins in
Plasma Proteome 39-40 distributions 44-45
E
edit
users 22
emails 19 EncyclopeDIA 92 Enrichment 72
F
field descriptions 76, 83 fields, custom 12
file extensions 15
file formats 15, 17, 87 file management 28, 89 file names 15
Filtered PPI Network 71 filters 53-56, 77, 89 folders 28, 89-91 functions 9, 41
G
Graph Colors preference 40
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Index
Graph Types preference 46 graphs 20
group analysis
differences between groups 66 Group Analysis
Box Plots section 73
Clustered Heatmap section 68 Coverage section 70 Enrichment section 72
Filtered PPI Network section 71 Raw Data section 66
Volcano section 69
Group Analysis tab 60, 66 grouping data 20
H
Heatmap 67
help, technical 102
Hierarchical Clustering 52
historical means 56
Horizontal Bar Position preference 41
I
icons 86
ICS 15
identification rates 45
index 39
injection 54-55
input files 24-25, 28, 79, 82, 93 instruments 15, 45, 54, 57-58, 76 intensities 39, 46
Intensities 44-45
Intensity Plot 67
interpreation of analysis results 60 intersections 40
J
Jaccard index 42-43 L
labels 37-38, 44
Lamppost Proteins’ Concentration 46-47 landmark proteins 46-47
layouts 37, 44
LC-MS 9, 45
LCLs 56
light theme 19
line graphs 37-38, 46
link, PAS 10
links 19
log10 39, 46
logs 86-87
lower control limits 56
M
mass spec controls 18, 54, 56 matrices 40, 42
MaxQuant 92
MaxQuant analysis protocol 92 means 37, 49, 56
method runs 76
metrics, displaying 34, 36, 46 miscleavage rates 45 moving files 89
MPE controls 18, 54
MS computer 91
MS controls 18, 54
MS data files 19, 28, 31, 40
automatic upload 91
file formats 15
file names 15
links 19, 24, 89
number of 86
removing 19, 25, 28, 79, 90
MS database 15, 39, 45, 92
MS file’s name length preference 41
N
n-values 39 nanoparticles 49-50, 76 navigation 9
O
optional inputs 26-27, 29-31, 57 orange, meaning 55
outliers 56
output files 57-59
oxidation ratios 45 P
Page Chart Layout preference 40, 42, 45- 46
pages
Analyses 86
Data Files 89
Plates 76
Projects 83
Protocols 92
Users and Permissions 21
parameter files 93 PAS link 10
PC1 48
PC2 48
PCA Analysis 48
PCC 42
Pearson correlation coefficient 42 Pearson’s correlation coefficient 43 Peptide Collection Plate
contents 76
peptide counts 50
Peptide Counts 38-39
Peptide Counts Distribution 49 Peptide Counts of Nanoparticles 50-51 peptides 37-38, 45
performance 44, 55
permissions 21
Plate Grid section 81
plate map files 15, 79
Plate Map Grid 46
Plate Samples tables 77, 80
plates
contents 15, 76 naming 26, 29, 77 removing 77
Plates page 9, 25, 76 Plates table 76
PPI Network 71 preferences
Distribution of Detected Proteins in Plasma Proteome 40
Intensities 45
Lamppost Proteins’ Concentration 47 PCA Analysis 48
Peptide Counts 39
Plate Map Grid 46
Protein Group and Peptide Counts of
Nanoparticles 51 Protein Group Counts 38
Protein Group Overlap Sets 41
Sample Comparability 42 principal component analysis 48 process controls 18, 53-54 projects
creating 26, 29, 79-80, 83-84 removing 84
revising 85
Projects page 9, 31, 83
Projects table 83
Protein Group Counts 37-38
Protein Group Counts Distribution 49 Protein Group Counts of
Nanoparticles 50-51 Protein Group Overlap Sets 40-41 protein groups 37, 40, 45
comparisons 42
intersections 40 protein names 40, 46-47 proteins 39
adding 47 annotated 40 counts 49 distribution 39-40 highlighting 40
Proteins preference 40 Proteograph Assay method
output 76
Proteograph Instrument Control
Software 15 proteome 40
Protocols page 92
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100

Index
Q
QC charts 34, 54-55
quality control 44, 47, 54, 66 quantification 45
quantiles 40, 44
Quantiles preference 40 quartiles 44-45
R
ranges, control limits 56 Raw Data 66
reanalyzing data 24, 31
red proteins 39
reference peptides 18 reference samples 18 references 39, 92
renaming files 89
renaming folders 90 required columns 25, 28, 79 results 9, 34, 36
results files 17, 34
results, interpretation of 60 runs 37, 76
S
Sample Comparability 42
sample description files 15, 79-80 sample information 16, 26, 29, 37, 82-83 samples
adding 83
analyzing 27, 30-31 correlations 42
grid view 81
nanoparticles 50
number of peptides 38, 45 number of proteins 39, 45 reviewing 77, 81-82 similar 48, 52
table view 81
92 sidebar 9
Similarity Score preference 43 similarity scores 42
sorting 20, 77
starting analysis 26, 29, 79-80, 83 starting points 25, 28, 31
status, analysis 86 summaries 53, 57-58 Summary 37
T
table view 82 tables
adjusting 77
teal, meaning 55-56
technical assistance 102
templates 25, 28, 79
tenants 14
theme 19
trends 37
turn two-factor authentication on or off 20 two-factor authentication 19
U
UCLs 56
upper control limits 56 user groups 55
user interface 9
customizing 19-20, 37, 41, 44 light or dark 19
navigation 9
scaling 46
User menu 21
user roles 21
Users and Permissions page 21 Users menu 21
Users page 9, 21
V
Vertical Height Rate preference 41 violin plots 44-45
Volcano 69
X
X Tick Label preference 38-39 Y
Y Axis Range preference 38-39, 51, 55 yellow wells 77, 81
scaling 46
Scaling preference 46
scatter plots 48, 50
search engine 9, 92
search engine parameters 93
Search field 21, 66, 76, 78, 83-84, 86, 92 search parameters 15, 92
search results 17
Seer contact information 102
Set Plate Map Grid 45
settings 37, 40, 44, 54-55
Default Analysis Protocol 19
Receive email notifications on analysis
updates 19
Remove MS data files when plate is
deleted 19
Use Authenticator App 19
Show/Hide dropdown 76, 78, 83-84, 86,
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Technical Support
For technical assistance, contact Seer.
Contact Information
Seer, Inc.
3800 Bridge Pkwy #102 Redwood City, CA 94065 Email: support@seer.bio
seer.bio
Telephone
650.453.0000
Proteograph Analysis Suite User Guide (CF-1003 B , PAS version 1.5) 102

Seer, Inc.
3800 Bridge Pkwy #102 Redwood City, CA 94065 650.453.0000 info@seer.bio
seer.bio