Considering Measurement Time and Depth in diaPASEF Plasma Proteomics.

ABSTRACT: Mass spectrometry (MS)-based plasma proteomics is a powerful approach to unraveling the biology or pathophysiology in large clinical cohorts. Implementation of data-independent acquisition in combination with ion mobility approaches (diaPASEF) has enabled high-throughput analysis with increasing proteomic depth. DIA-based methods are dependent upon experimental or in-silico-generated spectral libraries, yet there is a lack of consensus in the field about which library produces superior results in regard to protein and peptide identifications and quantifications. Here, we evaluated approaches for building a spectral library in plasma proteomics on a timsTOF HT system. Furthermore, the relationship between measurement time, library depth, and number of protein and peptide identification for

SUBMITTER: Smit ER 

PROVIDER: S-EPMC12604034 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature