PXD069212-1

PXD069212 is an original dataset announced via ProteomeXchange.

Title	Impact of variations in standard operating procedure on plasma proteome recovery
Description	Advancements in mass spectrometry and complementary technologies now enable comprehensive and high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease informative biomarkers. Commercial sources of non-diseased, healthy donor plasma samples are often used for proteomic workflow development and as controls for clinical studies. The overarching assumption is that standard operating procedures for plasma preparations are comparable across variable sources. In this study, we investigated the effectiveness of a particle-based protein enrichment strategy against a conventional proteomics workflow on plasma samples from 5 commonly used sources aiming to characterize the extent of variability when factors such as freeze-thaw cycles, anticoagulant, and operator-to-operator performance were controlled. Plasma samples were analyzed in data-independent acquisition mode using two distinct instruments (Exploris 480, timsTOF HT) and search algorithms (CHIMERYS, DIA-NN). Plasma proteome enrichment yields ranged from 4.5 to 8-fold more compared to the conventional workflow, achieving yields exceeding 5,000 proteins. Notably, the observer variability in proteome composition was largely attributable to differences in whole blood-to-plasma operating procedures across the sources. While these distinct proteomes remained undetectable with conventional workflows, particle-dependent proteome profiling successfully revealed the procedural differences.
HostingRepository	PRIDE
AnnounceDate	2026-04-13
AnnouncementXML	Submission_2026-04-12_18:53:10.211.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD069212
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sasha Singh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-08 12:09:41	ID requested
⏵ 1	2026-04-12 18:53:11	announced

10.1021/acs.jproteome.5c01012;

Kasai T, Weiss L, Wohlfahrt J, Matamalas JT, Shlayen G, Kirsch ZJ, Aikawa M, Aikawa E, Singh SA, Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery. J Proteome Res, 25(4):1941-1950(2026) [pubmed]

10.6019/PXD069212;

submitter keyword: mass spectrometry, clinical proteomics, biofluids,data-independent acquisition

Masanori Aikawa
contact affiliation	Yoshihiro Miwa Distinguished Chair & Founding Director, Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women’s Hospital; Professor of Medicine, Harvard Medical School
contact email	MAIKAWA@BWH.HARVARD.EDU
lab head
Sasha Singh
contact affiliation	Brigham and Women's Hospital, Harvard Medical School
contact email	sasingh@bwh.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD069212
     1. Label: PRIDE project
     2. Name: Impact of variations in standard operating procedure on plasma proteome recovery