Publications & Resource Library

Oncology Research Applications for Unbiased Proteomics

Jul 18, 2024  |  Research Guide Explore unbiased proteomics in cancer research for biomarker discovery and personalized medicine.

Model Organism Proteomics With the Species-Agnostic Proteograph XT

Jun 27, 2024  |  Application Note This application note demonstrates how the Proteograph XT workflow enhances protein detection in model organisms with deep and unbiased proteomic analysis, even from minimal sample volumes, without the need for preprocessing.

Integrating the SP100 Automation Instrument

Jun 27, 2024  |  One Sheet This one-sheet provides key details for integrating the SP100 Automation Instrument into your lab, including space requirements, peripheral equipment, and optimal operating conditions.

The Space Omics and Medical Atlas (SOMA) and International Astronaut Biobank

Jun 11, 2024  |  Publication This study presents the Space Omics and Medical Atlas (SOMA) and an international astronaut biobank, aiming to integrate multi-omics data from astronauts to advance space medicine and countermeasure development. It highlights the importance of comprehensive biobanking for understanding spaceflight's impact on human health.

Secretome Profiling Reveals Acute Changes in Oxidative Stress, Brain Homeostasis, and Coagulation Following Short-Duration Spaceflight

Jun 11, 2024  |  Publication This study profiles plasma proteins, metabolites, and extracellular vesicles from the SpaceX Inspiration4 crew, revealing significant changes in coagulation, oxidative stress, and brain-enriched proteins post-flight. It highlights how even short-duration spaceflight can disrupt human and murine physiology.

A Genome-Wide Association Study of Mass Spectrometry Proteomics Using the Seer Proteograph Platform

Jun 1, 2024  |  Preprint This study utilizes the MS-based Seer Proteograph platform for a genome-wide association study (GWAS) with proteomics on a diverse cohort. It identified and replicated numerous protein quantitative trait loci (pQTLs), showcasing the platform's ability to overcome limitations of affinity proteomics and discover new pQTLs not accessible before.

An Inflection Point in High-Throughput Proteomics With Orbitrap Astral: Analysis of Biofluids, Cells, and Tissues

Apr 27, 2024  |  Preprint This study introduces a comprehensive proteomics workflow integrating Orbitrap and Astral mass analyzers. The workflow enhances high-throughput and reproducibility across diverse sample types, facilitating biomarker discovery and disease pathology studies.

Deep, Unbiased and Quantitative Mass Spectrometry-Based Plasma Proteome Analysis of Individual Responses to mRNA COVID-19 Vaccine

Apr 23, 2024  |  Preprint This study combines a nanoparticle-based proteomic workflow with tandem mass tag labeling to analyze proteomic changes in response to the Pfizer-BioNTech mRNA COVID-19 vaccine. It identifies significant protein variations in individuals, providing insights into the molecular mechanisms driving diverse immune responses to vaccination.

Frontiers in Plasma Proteome Profiling Platforms: Innovations and Applications

Apr 1, 2024  |  Publication This study compares workflows for plasma proteomic profiling, identifying the SeerProteographXT workflow as superior in terms of depth, accuracy, and reproducibility. It demonstrates the workflow’s application across various biofluids, enhancing large cohort studies in biomarker discovery.

Harnessing the Power of Proteomics in Precision Diabetes Medicine

Feb 12, 2024  |  Publication This study explores the use of proteomics in precision diabetes medicine, highlighting its potential for identifying biomarkers and understanding disease mechanisms, ultimately aiming to improve diabetes diagnosis and treatment.

1.4 min Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry

Feb 8, 2024  |  Preprint This study introduces a hybrid method integrating direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein coronas enrichment. This method allows for high throughput and efficient plasma proteomic profiling, identifying over 280 proteins in 1.4 minutes, and has the potential to process approximately 1,000 samples daily.

Recent Developments in Mass-Spectrometry-Based Targeted Proteomics of Clinical Cancer Biomarkers

Jan 30, 2024  |  Publication This review discusses the application of targeted proteomics in cancer, highlighting workflows, clinical validation requirements, and recent advancements. The study underscores the advantages and challenges of using mass spectrometry-based assays for clinical cancer biomarker analysis.

timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery

Jan 15, 2024  |  Publication Evaluation of the qualitative and quantitative performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for analysis of neat plasma samples and plasma samples processed using the Proteograph Product Suite.

Identification of Novel Biomarkers for Alzheimer’s Disease and Related Dementias Using Unbiased Plasma Proteomics

Jan 8, 2024  |  Preprint This study leverages mass spectrometry proteomics to identify novel blood-based biomarkers for Alzheimer’s disease. By analyzing 1,786 plasma samples from 1,005 patients, the study identifies differentially abundant proteins, providing opportunities for earlier, targeted interventions.

Unbiased and Deep Proteomic Analysis of Secretome Samples Using the Proteograph XT Workflow

Jan 4, 2024  |  Application Note This application note illustrates the capability of the Proteograph XT workflow for comprehensive proteomic characterization of conditioned media secretomes, highlighting advantages achieved without the need for traditional preprocessing and sample manipulation protocols.

Multi-Omics Profiling With Untargeted Proteomics for Blood-Based Early Detection of Lung Cancer

Jan 4, 2024  |  Preprint Shedding new light into how we diagnose lung cancer, this is one of the largest multi-omics observational studies with extensive, untargeted plasma proteomics analysis at scale.

OMICmAge: An Integrative Multi-Omics Approach to Quantify Biological Age With Electronic Medical Records

Oct 23, 2023  |  Preprint The study helped develop OMICmAge, integrating DNA methylation and multi-omics data to quantify biological age. The Proteograph platform was leveraged to enhance protein detection and provide deep insights into the aging process.

Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH) Proteomics Workflow

Oct 16, 2023  |  Publication This study develops an optimized SWATH proteomics workflow to analyze plasma biomarkers in rheumatoid arthritis (RA) patients, identifying proteins related to systemic inflammation and other RA-related processes. The workflow enhances data quality and proteome coverage, providing deeper insights into RA pathology.

Comprehensive and Automated Profiling of Host Cell Proteins Using Proteograph XT Workflow

Oct 12, 2023  |  Application Note This application note shows how the Proteograph XT platform increases discovery depth, simplifies HCP MS sample prep workflow and compares with peer-reviewed articles to benchmark the Protegraph XT performances using the NIST 8671 mAB.

The Effects of Resistance Training on Denervated Myofibers, Senescent Cells, and Associated Protein Markers in Middle-Aged Adults

Oct 6, 2023  |  Publication This study investigates the effects of resistance training on denervated myofibers, senescent cells, and associated protein markers in middle-aged participants. It finds that resistance training upregulates proteins related to muscle-nerve communication but does not significantly alter denervated myofibers or senescent cells.

Longitudinal Deep Multi-Omics Profiling in a CLN3Δex7/8 Minipig Model Reveals Novel Biomarker Signatures for Batten Disease

Sep 22, 2023  |  Preprint This study used a deep multi-omics approach to discover new biomarkers using longitudinal serum samples from a porcine model of CLN3 disease.

Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics

Aug 29, 2023  |  Preprint The Proteograph XT Assay workflow with the Orbitrap Exploris 480 MS by Thermo Fisher Scientific, demonstrated unprecedented depth, reproducibility, and throughput - providing researchers with the ability to amplify their proteomics research discovery power.

A Novel Deep Proteomic Approach in Human Skeletal Muscle Unveils Distinct Molecular Signatures Affected by Aging and Resistance Training

Jul 5, 2023  |  Publication In this breakthrough research with Auburn University, we implemented a novel study technique to potentially offer new insights into the molecular intricacies of aging and the effects of aging and resistance training on protein levels.

Large-Scale Plasma Proteomics With the Proteograph XT Workflow

Jun 16, 2023  |  Technical Note This technical note shows how any lab can process hundreds of samples quickly and with confidence with the Proteograph XT assay kit.

Accelerating Throughput With the Proteograph XT Assay

Jun 16, 2023  |  Application Note This application note shows how the Proteograph method increases discovery power, and our scalable data management allows for simplified processing and analysis.

Why Unbiased Proteomics Is Necessary

May 31, 2023  |  Research Guide Discover why deep, rapid, unbiased proteomics is critical for advancing our understanding of health and biology.

Evaluation of Deep Plasma Proteomic Analysis With the Proteograph Workflow and TMT Sample Labeling

Apr 28, 2023  |  Technical Note This technical note describes the performance of the Proteograph workflow with TMT sample labeling compared to the data dependent acquisition method for label-free quantification.

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

Apr 21, 2023  |  Publication This study uses the Proteograph™ Product Suite to perform a pQTL analysis, and highlights the advantages of Proteograph workflow for identifiying protein altering variants with clinical relevance that may not be detectable using affinity-based methods.

Functionally Distinct BMP1 Isoforms Show an Opposite Pattern of Abundance in Plasma from Non-Small Cell Lung Cancer Subjects and Controls

Mar 29, 2023  |  Publication Identification of protein isoforms in a non-small cell lung cancer cohort shows functionally distinct, cancer- and control-associated isoforms, including BMP1. This article demonstrates the utility of combined unbiased proteomics with transcriptomic analysis, and identified over 400 subject-specific protein variants, showing how the Proteograph Product Suite can support proteogenomics studies.

Balancing Deep Proteome Coverage with Limited Sample Amounts Using the Proteograph Product Suite

Feb 28, 2023  |  Application Note This application note provides a framework for understanding Proteograph performance when limited starting sample volumes are used.

Evaluation of Blood-Based Sample Types for Deep Plasma Proteomics

Feb 28, 2023  |  Application Note This application note explores how deep and unbiased proteomics analysis reveals differences between serum and plasma proteomes

Integrated Plasma Multi-Omics Using Nanoparticle Technology and Single-Shot Capillary MS

Dec 14, 2022  |  Customer Poster This poster demonstrates how the Proteograph workflow enables, deep, and rapid multi-omic analysis of plasma in a study that resulted in ~5X better protein groups coverage versus neat plasma digestion workflow with a single injection DDA LC-MS workflow with FAIMS Pro interface on the Orbitrap MS system.

A Highly-Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Signatures Using Proteograph Technology With Trapped Ion Mobility Mass Spectrometry

Dec 14, 2022  |  Customer Poster This poster highlights current challenges in large-scale DIA data analysis and evaluates the impact of various spectral library approaches. The study leverages the Proteograph workflow and Bruker timsTOF platforms to investigate ~900 patient serum samples with controls.

Proteograph Service Plans

Nov 11, 2022  |  Brochure A brochure describing different options for extended warranty Proteograph Service Plans.

Human Plasma Sample Preparation Workflow Using the Proteograph Product Suite

Oct 4, 2022  |  Technical Note A technical note describing the Proteograph Product Suite and workflow for complete plasma proteomics sample preparation using the SP100 automation instrument.

Ultra-High Coverage of the Serum Proteome Using a Multi-Nanoparticle Based Workflow

Jun 24, 2022  |  Customer Poster This poster demonstrates ultra-high coverage of serum proteins with over 5,000 protein groups identified in a 105-sample cohort and over 3,000 protein groups identified on average per sample. Proteins were quantified at 3-5 fold higher levels compared to depleted and un-depleted serum, with 30% enhanced coverage of low abundant cytokines. This data supports a comprehensive serum proteomics workflow that can be used for patient stratification as well as potential identification of novel biomarkers which are not accessible through other strategies.

An Unbiased Multi-Omics Approach for the Detection of Pancreatic Cancer Biomarkers Utilizing Ion-Mobility Mass Spec and Nanoparticle-Based Proteograph Technology

Jun 24, 2022  |  Customer Poster This poster describes a multi-omics platform facilitating the evaluation of the global proteome and lipidome in a pancreatic cancer cohort and identified multiple putative biomarker candidates across analyte classes for early disease detection.

Deep Profiling of the Spaceflight Plasma Proteome Reveals Changes in Reactive Oxygen Species, Telomeric DNA Binding, and Ribosomal Assembly and Biogenesis

Jun 24, 2022  |  Customer Poster This poster demonstrates how comprehensive plasma proteomics profiling of the first all-civilian astronaut crew using the Proteograph Product Suite coupled with LC-MS analysis that offers unique insights to the impact of spaceflight on human health demonstrating even short-term spaceflights can have an impact on human physiology which needs further investigation and monitoring.

Incorporation of Glycoproteome Detection into Large Scale Unbiased Proteomics Studies Utilizing Nanoparticles

Mar 29, 2022  |  Customer Poster This poster, presented at USHUPO from Prognomiq describes how Seer’s Proteograph™ nanoparticle technology specifically captures unique proteoforms in the corona formation and allow for comprehensive assessment of the circulating glycoproteome.

Engineered Nanoparticles Enable Deep Proteomics Studies at Scale by Leveraging Tunable Nano–Bio Interactions

Mar 15, 2022  |  Publication This study examines in detail the relationship between the unique physicochemical properties of a panel of proprietary engineered nanoparticles (NPs) and the diverse pattern of protein sampling that is enabled by a unique nano-bio interface that is created between a given NP surface and a given biological sample.

Enhanced Competition at the Nano-Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes

Jan 13, 2022  |  Publication This article explores the unique capacity of nanoparticles, a key component of the Proteograph Product Suite, to be tuned to interact with proteins by tailored surface functionalization and optimized to enable deeper protein access.

The Utility of Nanoparticle Protein Coronas for Studying the Plasma Glycoproteome

Nov 9, 2021  |  Customer Poster This collaboration between Seer and Protein Metrics presented at the American Society for Mass Spectrometry describes the formation of NP protein coronas that enable analysis of subpopulations of the glycoproteome without the need for subsequent, glycopeptide-specific enrichment.

Nanoparticle-Based Method Identifies 2,200 Proteins in a Cardiovascular Disease Study Covering Known Biomarkers Among Other Differentially Expressed Proteins

Nov 9, 2021  |  Customer Poster This collaboration with the Broad Institute presented at the American Society for Mass Spectrometry describes a Proteograph™ application for cardiovascular biomarker research using deep plasma proteomics. Over 2000 proteins were detected in each individual patient sample with a total of over 4000 across 16 samples.

Proteograph Analysis Suite Brochure

Oct 18, 2021  |  Brochure An overview of the Proteograph Analysis Suite, a dedicated software solution for processing, analyzing, and visualizing proteomics data sets generated by LC-MS, including the new proteogenomics workflow.

Proteograph Product Suite Brochure

Mar 31, 2021  |  Brochure An overview of the Proteograph Product Suite, Seer's proprietary engineered nanoparticle technology and the applications enabled by this solution.

Rapid, Deep and Precise Profiling of the Plasma Proteome With Multi-Nanoparticle Protein Corona

Jul 22, 2020  |  Publication This Nature Communications paper demonstrates that Proteograph technology is unmatched in its combination of depth, breadth, and speed—creating the necessary scale for proteomics profiling studies that lead to unprecedented discovery.