Browse our recent publications


Deep plasma protein profiling in Alzheimer’s disease (AD) with a novel unbiased and scalable proteogenomics approach

Deep plasma protein profiling in Alzheimer’s disease (AD) with a novel unbiased and scalable proteogenomics approach

This poster demonstrates how the Proteograph™ workflow offers deep, broad, and rapid processing of samples to enable large and more powerful studies per unit time and resource. The 200 subject Alzheimer (AD) cohort study was processed in approximately three weeks and generated unbiased proteomics data of over 5,000 proteins as well as identified new targets as well as known targets and pathways implicated in AD. The data from both acquisition schemes was equally powerful for both classifications of disease state, identifying pQTLs with DIA to provide 2X higher sample analysis throughput.
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Dec
2022

Applications:
Neurodegenerative Disease

Product: proteograph

A large scale multi-cancer, multi-omics biomarker study of >1,800 subjects incorporating deep unbiased plasma proteomics

A large scale multi-cancer, multi-omics biomarker study of >1,800 subjects incorporating deep unbiased plasma proteomics

This poster demonstrates how Liquid-Chromatography-Mass Spectrometry (LC-MS) based plasma proteomics technologies are now capable of providing deep proteome coverage with sufficient reproducibility, robustness, and throughput. This study highlights the importance of plasma proteomics in a large multi-omics biomarker discovery study of >1800 samples with >3900 protein groups IDs using the Proteograph workflow and Bruker timsTOF.
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Dec
2022

Applications:
Cancer Research

Product: proteograph

Matrix-matched calibration curves provide verification of quantitative data-independent acquisition techniques for deep plasma proteomics

Matrix-matched calibration curves provide verification of quantitative data-independent acquisition techniques for deep plasma proteomics

This poster demonstrates how the Proteograph™️ Product Suite, combined with DIA LC-MS on Orbitrap Exploris 480 MS, enables quantitative plasma proteomics with depth and scale. Seer’s multi-nanoparticle workflow uniquely enables deep, unbiased biomarker discovery in biofluids to offer significant opportunities for protein biomarker discovery at scale.
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Dec
2022

Applications:
Computational Method

Product: proteograph

Experimental and computational approach to profile nanoparticle-protein interactions for deep plasma proteomics

Experimental and computational approach to profile nanoparticle-protein interactions for deep plasma proteomics

This poster highlights recent Seer's research (published in Advanced Materials) on the dynamics of protein corona formation around nanoparticles. By measuring the individual dynamics of unprecedented 3200 plasma proteins, this work paves the road for quantitative modeling of nano-bio interactions at the molecular level, streamlining the design of novel nanoparticles and further enhancing protein quantification. The latter is exemplified by successful application of machine learning to reconstruct absolute protein intensities in neat plasma from the NP-protein profiles.
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Dec
2022

Applications:
Computational Method

Product: proteograph

Deep and unbiased proteomics analysis reveals differences between serum and plasma proteome in matched donors

Deep and unbiased proteomics analysis reveals differences between serum and plasma proteome in matched donors

This poster demonstrates how the Proteograph™ workflow provides deeper coverage of the proteome compared to neat plasma/serum digestion workflow, enabling differentiations of sample types with higher resolution. The study evaluated different blood-based sample types for deep blood-based proteomics analysis, highlighting the difference between plasma and serum proteomics and the importance of using a single sample type in large-scale biomarker discovery studies, or additional consideration to be made for sample-type differences.
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Dec
2022

Applications:
Assay Method

Product: proteograph

The nanoparticle-based plasma proteomics workflow enables the investigation of glycoproteome

The nanoparticle-based plasma proteomics workflow enables the investigation of glycoproteome

This study evaluates Seer’s multi nanoparticles- based Proteograph workflow performance compared to neat plasma workflow in capturing glycoproteins and a conventional glycol-enrichment workflow using magnetic Fe-NTA beads. This poster demonstrates how by compressing the dynamic range and making the low abundance proteins and corresponding peptides more visible to the downstream LC-MS, nanoparticles can facilitate the detection of peptides with increased sensitivity and more efficiency, significantly enhancing the coverage of these proteins in blood plasma even without subsequent enrichment.
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Dec
2022

Applications:
Assay Method

Product: proteograph

Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and deep coverage of proteomes

Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and deep coverage of proteomes

This poster demonstrates how nanoparticle coronas provide deep coverage of biological content, including the identification of low abundant cytokines and chemokines, and post-translationally modified peptides. Understanding the nanoparticle-protein interactions on the quantitative level enables the design of NP-based assays to interrogate specific physicochemical fraction of the proteome occupied by hundreds to thousands of proteoforms.
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Dec
2022

Applications:
Assay Method

Product: proteograph

A cloud-scalable software suite for large-scale proteogenomics data analysis and visualization

A cloud-scalable software suite for large-scale proteogenomics data analysis and visualization

This poster demonstrates how the Proteograph™ Analysis Suite (PAS) is a comprehensive proteogenomic software application that enables user-friendly and reproducible multi-omic analyses of proteomic and genomic data at scale. The cloud-based solution, capable of completing data analysis of ~200 sample proteomics in approximately five and a half hours, allows researchers to process, analyze, and visualize proteomics data sets generated by Liquid Chromatography-Mass Spectrometry (LC-MS).
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Dec
2022

Applications:
Software

Product: proteograph

A highly-scaled proteomic discovery study for prostate cancer diagnostic signatures using Proteograph technology with trapped ion mobility mass spectrometry

A highly-scaled proteomic discovery study for prostate cancer diagnostic signatures using Proteograph technology with trapped ion mobility mass spectrometry

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.
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Dec
2022

Applications:
Cancer Research

Product: proteograph

Integrated plasma multi-omics using nanoparticle technology and single-shot capillary MS

Integrated plasma multi-omics using nanoparticle technology and single-shot capillary MS

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.
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Dec
2022

Applications:
Assay Method

Product: proteograph