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

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 sources. In this study, we investigated the effectiveness of a particle-based protein enrichment strategy against a conventional proteomics workflow on plasma samples from five commonly used commercial sources. We aimed to characterize the extent of variability in plasma proteomes when factors such as freeze-thaw cycles, choice of anticoagulant, and operator-to-operator performance were accounted for in the study setup. Plasma samples were analyzed in data-independent acquisition mode by using two distinct instruments (Exploris 480, timsTOF HT) and search algorithms (CHIMERYS, DIA-NN). Plasma proteome enrichment yields ranged from 2.8- to 6.2-fold more compared to the conventional workflow, achieving yields exceeding 5000 proteins (timsTOF HT). Notably, the observed variability in proteome composition was largely attributable to differences in whole blood-to-plasma operating procedures across commercial sources. While these distinct proteomes remained undetectable with conventional workflows, particle-dependent proteome profiling successfully revealed the procedural differences.