Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

ABSTRACT: Consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is a prerequisite for functional analysis of biological processes. Data-independent acquisition (DIA) is a bottom-up mass spectrometry approach that provides complete information on precursor and fragment ions. However, owing to the convoluted structure of DIA data sets, confident, systematic identification and quantification of peptidoforms has remained challenging. Here, we present inference of peptidoforms (IPF), a fully automated algorithm that uses spectral libraries to query, validate and quantify peptidoforms in DIA data sets. The method was developed on data acquired by the DIA method SWATH-MS and benchmarked using a synthetic phosphopeptide reference data set and phosph

SUBMITTER: Rosenberger G 

PROVIDER: S-EPMC5593115 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature