Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set.

ABSTRACT: Human plasma is routinely collected during clinical care and constitutes a rich source of biomarkers for diagnostics and patient stratification. Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a key method for plasma biomarker discovery, but the high dynamic range of plasma proteins poses significant challenges for MS analysis and data processing. To benchmark the quantitative performance of neat plasma analysis, we introduce a multispecies sample set based on a human tryptic plasma digest containing varying low level spike-ins of yeast and E. coli tryptic proteome digests, termed PYE. By analysing the sample set on state-of-the-art LC-MS platforms across twelve different sites in data-dependent (DDA) and data-independent acquisition (DIA) modes, we provide a data resou

SUBMITTER: Distler U 

PROVIDER: S-EPMC12491457 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature