Msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease.

ABSTRACT:

Summary

Identification and quantification of phosphorylation sites are essential for biological interpretation of a phosphoproteomics experiment. For data independent acquisition mass spectrometry-based (DIA-MS) phosphoproteomics, extracting a site-level report from the output of current processing software is not straightforward as multiple peptides might contribute to a single site, multiple phosphorylation sites can occur on the same peptides, and protein isoforms complicate site specification. Currently only limited support is available from a commercial software package via a platform-specific solution with a rather simple site quantification method. Here, we present sitereport, a software tool implemented in an extendable Python package called msproteomics to report phosphosi

SUBMITTER: Pham TV 

PROVIDER: S-EPMC11239223 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature