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Benchmarking plasma proteomics depletion and enrichment workflows prior to LC-MS/MS analysis

ABSTRACT: A plasma sample was prepared using multiple depletion and enrichment techniques in order to improve the depth of proteomics analyses.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD069187 | Pride | 2026-06-15

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	A00513_Neat_1.raw	Raw
	A00514_Neat_2.raw	Raw
	A00515_Neat_3.raw	Raw
	A00516_ID_1.raw	Raw
	A00517_ID_2.raw	Raw

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Publications

Systematic Evaluation of Depletion and Enrichment Technologies for Platelet-Free Plasma Proteomics.

Al Siblani Salem S Armengaud Jean J Lozano Clément C

Journal of proteome research 20260317 6

Plasma proteomics is a rapid, noninvasive, and highly informative approach for identifying disease biomarkers. However, the wide dynamic range of protein concentration limits the depth of liquid chromatography-tandem mass spectrometry proteomics. To address this challenge, we evaluated, with an Orbitrap Astral instrument using DIA, the performance of several protein depleting and enriching technologies on platelet-free plasma. Specifically, we assessed: perchloric acid depletion, immunodepletion ...[more]

PMID: 41842586

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Project description:In this project we asses 5 different sample processing workflows for mass spectrometry based plasma proteomics and compare the results with a neat plasma workflow. The workflows evaluated includes protocols for abundant protein depletion (Top14 most abundant protein depletion and protein precipitation by perchloric acid) and enrichment for low abundant proteins (SAX based enrichment of low abundant proteins and ultracentrifugation based enrichment for extracellular vesicles). The assessment comprises two steps: In the first step, each workflow is repeated 8X on the same input material from one donor and focuses on proteomic depth and precision of protein quantifications. In addition, the effect of three different input materials in the form of platelet poor plasma (PPP), platelet rich plasma (PRP) and serum (SER) is evaluated. In the second step, samples from 72 healthy donors is evaluated 1X in SER and in PPP or PRP, and in addition, levels of 10 proteins--commonly measured in clinical practise and spanning 5 orders of magnitude in abundance--is quantified by a clinical rutine measurement performed at a Cobas system. Focus is again proteomic depth obtained by the evaluated methods, and in addition focus is on how well the estimates by the clinical rutine measurements in SER correlate with the mass spectrometry based estimates after sample processing by the 6 assessed workflows in all three input types (PPP. PRP, SER).

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Benchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry

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