Dataset Information

Impact of variations in standard operating procedure on plasma proteome recovery

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Sasha Singh

LAB HEAD: Masanori Aikawa

PROVIDER: PXD069212 | Pride | 2026-04-13

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	01_TK_ENplus_Hu_Plasma_DIA_30min_Source-1-5_combined.mzML	Mzml
	01_TK_ENplus_Hu_Plasma_DIA_30min_Source-1-5_combined.mzid	Mzid
	01_TK_ENplus_Hu_Plasma_DIA_30min_Source-1-5_combined.pdResult	Other
	01_TK_ENplus_Hu_Plasma_DIA_30min_Source-1_1-12.mzML	Mzml
	01_TK_ENplus_Hu_Plasma_DIA_30min_Source-1_1-12.mzid	Mzid

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Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery.

Kasai Taku T Weiss Luisa L Wohlfahrt Jessica J Matamalas Joan T JT Shlayen Gabriel G Kirsch Zachary J ZJ Aikawa Masanori M Aikawa Elena E Singh Sasha A SA

Journal of proteome research 20260325 4

Advancements in mass spectrometry and complementary technologies now enable comprehensive, high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease-informative biomarkers. Commercial sources of nondiseased, 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 preparation are comparable across different so ...[more]

PMID: 41879802

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