Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.

ABSTRACT: Mass spectrometry based targeted proteomics methods provide a sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semistochastic sampling, or empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of the peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific inf

SUBMITTER: Plubell DL 

PROVIDER: S-EPMC12310296 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature