Linfeng Wu (Santa Clara, CA / US), Daniel Cuthbertson (Denver, CO / US), Wolfgang Mayser (Waldbronn / DE)
The advancement of triple quadrupole LC/MS systems and the publicly available peptide MS/MS spectral libraries have enabled researchers to develop comprehensive MRM-based assays without performing extensive proteome identifications in the first place.
In this study, we performed a proof-of-concept study in healthy human plasma samples using Uniprot human reference proteome, PeptideAtlas plasma spectral libraries, Skyline software and Agilent 6495D LC/TQ system. A comprehensive peptide quantitative assay was developed quickly based on publicly available libraries without using stable isotope-labeled standard peptides (SILs). The final optimized dynamic MRM method contain a 20-min linear LC gradient and covers 3604 MRM transitions presumptively matching to 390 plasma proteins and 846 peptides. This assay was applied to quantify plasma samples from 40 healthy human subjects (20 males and 20 females) for group comparison analysis. The results demonstrated that this rapid and economical workflow can discover protein biomarkers in complex cohort samples.