FAQ’s

• Dell OptiPlex 5080 Micro
• 10th Generation Intel Core i7-11700T (8-Core, 16MB Cache, 1.9GHz to 4.5GHz, 35W)
• Intel UHD Graphics 630
• Windows 10 Pro 64 English, French, Spanish
• No Microsoft Office License Included
• 8GB (1x8GB) DDR4 non-ECC Memory
• M.2 256 GB SOLID STATE HARD DRIVE OR BETER
• Internal Wireless Antennas
• Intel Wi-Fi 6 AX201, Dual-band 2×2 802.11ax with Bluetooth 5.1
• Dell 24 Touch Monitor – P2418HT (touchscreen)

A Size 200 high pressure N2 cylinder will last approximately 20-25 Proteograph assays. We recommend changing the cylinder when at around 25% full to avoid low pressure errors during the assay and possible sample loss.

The Proteograph Product Suite features the following products:

• SP100 Automation Instrument
• Intuitive Proteograph Instrument Control Software (ICS) for experiment setup and instrument operations
• Custom Proteograph Assay method that processes proteins into MS-ready peptides in a typical 8-hour workday
• Dedicated methods for instrument maintenance and troubleshooting
• Automated methods for peptide quantification and peptide reconstitution

Proteograph Assay Kit
A proprietary two-well panel of engineered nanoparticles, for processing up to 40 samples in one 96-well plate.
Buffers and reagents for protein denaturation, digestion, and peptide purification
Four quality controls to facilitate the comparison of results across different assays and troubleshooting for a specific assay

PQR Labware Kit
Contains all required labware used with SP100 Automation Instrument with automated peptide quantification and reconstitution methods. Enough labware for 4 runs. Designed to work with the Pierce Fluorometric Peptide Assay (sold separately by Thermo Fisher)

Proteograph Analysis Suite (PAS)
A dedicated software solution for processing, analysis, and visualization of proteomics data sets generated by liquid chromatography-mass spectrometry (LC-MS).
Software includes an integrated search engines for identification and annotation of LC-MS data

The table that comes with the SP100 is customized specifically for instrument stability and operation. Holes placed in the table are designed for critical access to gas lines and waste containers, while grooves in the table are critical for instrument stability and operational performance. We do not install the instrument on a user provided table.

The Proteograph Assay method can accommodate configurations of both 20 and 40 samples. Each sample is incubated in two separate wells with nanoparticles, resulting in 80 wells of peptides in a 96-well plate.

Yes, daily and weekly maintenance are a part of normal instrument operation. Maintenance protocols help to ensure optimal operating performance of the SP100 and ultimately successful processing of target samples. It is important to run the weekly maintenance protocol even during periods of instrument downtime, while the daily maintenance protocol should be run immediately prior to any instrument operation.

Yes, the SP100 Instrument should be powered off when not in use.

The total assay time including sample prep and method setup is 9 hours.

Peptide quantification of the samples and controls can serve as an indicator for a successful run.

Beyond the user guides, additional Proteograph Product Suite Training Videos can be found on YouTube.

Additional resources can be found through the support section of our website.

If you have any further questions regarding training, please contact Support@seer.bio

Yes, back to back assays can be ran during the same day to process a total of 80 samples (40 samples per assay) in one day. Users would need to be present for approximately 30-45 minutes at the beginning of each run for assay preparation and setup and for approximately 30 minutes at the end of each assay to ensure both peptide collection plate is properly stored, the deck is cleaned up, and for recommended peptide quantification immediately following assay completion.

No, daily maintenance can be performed at the start of each day. However, we would suggest running the MPE flush between consecutive assays in the same day.

Based on recommended starting volumes of 240 uLs, there may be approximately 40 uLs of sample remaining in the sample tubes. These samples will be left at ambient temperature for the duration of the assay. Seer does not recommend users removing samples in the middle of the runs as reaching behind the front cover when the robotic arms are in motion can pose a serious safety hazard for the operator.

Yes, currently the Proteograph assay is designed to run with the full nanoparticle panel resulting in two wells of collected peptides for each sample. Seer strongly recommends running the two injections per sample for mass spectrometry analysis to maximize the discovery capability. However, users can still decide on the number of injections per sample depending on their specific situation.

Seer recommends using a fluorescence-based quantitation method, such as the Pierce^TM Quantitative Fluorometric Peptide Assay (Thermo Fisher, Cat# 23290). Here is a link to this product with more information (https://www.thermofisher.com/order/catalog/product/23290?SID=srch-hj-23290#/23290?SID=srch-hj-23290). This kit is used in the automated peptide quantification method available on the SP100 platform. Other methods for peptide quantification may be used based on user needs. The automated peptide quantification that is available in the XT ICS software is designed based on the protocols of the PierceTM Quantitative Fluorometric Peptide Assay.

Yes, Seer recommends using a trap and elute setup when analyzing samples by LC-MS. While this is not required, we have seen increased longevity and stability of analytical columns and MS signal when using a compatible trap column upstream of the user selected analytical column.

We recommend annually scheduled Preventive Maintenance. Information about scheduled services can be found  here, or contact your Seer representative to learn more.

Seer has comprehensively analyzed plasma and serum samples on the SP100. Additional samples types, such as CSF, urine, synovial fluid, and cell culture media have also been tested. Please contact support@seer.bio for additional information.

Yes, please contact support@seer.bio to discuss running other sample types on the SP100.

240 μl per sample is needed.

Yes, please contact support@seer.bio to discuss running other sample types on the SP100.

No. The automated assay has been developed and optimized to be run on the SP100 only.

Any mass spectrometer instrument designed for proteomic analysis can fit seamlessly into the Proteograph workflow. Upon request, Seer can provide recommended methods for LC-MS implementation.

The first step of setting up an analysis depends on preference: start either on the Plates page by selecting Add Plate or on the Data Files page by selecting Link to Plate. Alternatively, you can start on the Projects page and select existing samples.

To reanalyze data analyzed using the Proteograph Analysis Suite, go to the Projects page, select the samples you want to reanalyze, and select Analyze. This option is useful for reanalyzing data using a different analysis method.

The Projects page offer two ways to start an analysis: Analyze and Analyze Controls. The Analyze button analyzes all selected samples in a project, including controls. The Analyze Controls button analyzes controls in the project only. Both buttons open a dialog where you can name the analysis, specify the analysis protocol, and input other general information.

The plate map file is a .csv file that specifies the location of each sample and control in a 96-well plate. The instrument control software (ICS) generates the file and automatically populates each column except MS file name. You must specify the MS data file name in the first column of the file, and then upload it to PAS during analysis setup.

The sample description file is an optional .csv file that a user may provide to indicate additional metadata (ie. condition, description, replicate, etc.). This file can be associated with a plate during plate addition or from the Plates page to an existing plate.

From the Analyses page, select a completed analysis and then select the ‘Group Analysis’ tab to review the quantitation results organized in groups according to the sample metadata. From this page, select the ‘Setup Group Analysis’ button to access a guided wizard that will setup the differential expression analysis of specific samples or groups of samples.

Proteograph assay controls and their analysis results are tracked separately on the ‘QC Charts’ tab. From this page key performance metrics are automatically recorded and can be quickly reviewed relative to control results from other plates or studies. Statistical limits are calculated based on historical data and displayed to evaluate deviations from expected ranges.

Analysis results can be exported by first selecting an analysis from the Analyses page, and then selecting the ‘Protein Group/Peptide Results’ button in the results tab. Results are exported as peptide and protein group .csv files.

The NP tables summarize LFQ results at the individual nanoparticle level. In the Panel tables, the single quantification value for a particular peptide or protein group represents the quantitation value of the NP measured most frequently across all samples (Max Representation roll-up)