Dataset Information

Benchmarking workflows for plasma proteomics

ABSTRACT: 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).

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma, Blood Serum

DISEASE(S): Disease Free

SUBMITTER: Ole Østergaard

LAB HEAD: Jesper Velgaard Olsen

PROVIDER: PXD070324 | Pride | 2026-05-04

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	01_Neat_Cohort_060SPD_147f.7z	Other
	01_Neat_Cohort_100SPD_145f.7z	Other
	01_Neat_QC_100SPD_24f.7z	Other
	01_Neat_QC_60SPD_24f.7z	Other
	02_PerCA_Cohort_060SPD_145f.7z	Other

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Publications

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

Kverneland Anders Handrup AH Østergaard Ole O Schmidt Luisa L Østergaard Johansen Mia M Ullitz Thorsen Steffen S Frikke Schmidt Ruth R Christoffersen Christina C Olsen Jesper Velgaard JV

Journal of proteome research 20260502

Plasma proteomics based on mass spectrometry has great potential for biomarker discovery. Plasma is challenging for mass spectrometry due to the high dynamic range in protein abundance. Several workflows have been developed to overcome this, and in this study, we compare prominent enrichment and depletion workflows using platelet-poor plasma (PPP), platelet-rich plasma (PRP), and serum (SER). Our results show that depletion workflows including Top14 depletion and acid precipitation allow quantif ...[more]

PMID: 42068309

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