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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Updated: May 4, 2026

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Published on: April 24, 2020

Benchmarking Plasma Proteomics Workflows and Their Correlation to Clinical Routine Protein Assays.

Anders Handrup Kverneland^1,2, Ole Østergaard^1,3, Luisa Schmidt^1,3

¹Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.

Journal of Proteome Research

|May 2, 2026

Summary

This summary is machine-generated.

Choosing the right plasma proteomics workflow is key for biomarker discovery. Depletion methods quantify different proteins than enrichment methods, impacting results for large cohorts and serum samples.

Keywords:

Cobas Orbitrap Astral biomarker discovery clinical proteomics extracellular vesicles plasma proteomics platelet-poor plasma platelet-rich plasma workflow assessment

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Area of Science:

Proteomics
Biomarker Discovery
Mass Spectrometry

Background:

Plasma proteomics is valuable for biomarker discovery but faces challenges due to high protein dynamic range.
Various enrichment and depletion workflows exist to address these challenges in mass spectrometry.

Purpose of the Study:

To compare prominent enrichment and depletion workflows for plasma proteomics.
To evaluate workflow performance using platelet-poor plasma (PPP), platelet-rich plasma (PRP), and serum (SER).

Main Methods:

Comparison of depletion workflows (Top14, acid precipitation) and enrichment workflows (bead-based, ultracentrifugation).
Analysis of proteome differences, quantitative performance, and correlation across sample types (PPP, PRP, SER).
Validation against clinical routine protein measurements.

Main Results:

Depletion and enrichment workflows quantify distinct proteomes.
Enrichment methods offer greater proteome depth and quantitative accuracy but may be less robust for large cohorts.
High correlation between PPP and PRP samples; lower correlation with SER, especially for enrichment methods.
Heterogeneous correlation with clinical assays; low-abundant proteins correlated well, while albumin and transferrin correlated poorly.

Conclusions:

Workflow selection for plasma proteomics should align with analytical goals and sample collection protocols.
Understanding workflow-specific biases is crucial for accurate biomarker discovery and interpretation.
The choice between depletion and enrichment depends on the desired proteome coverage and cohort size.