MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics.

ABSTRACT: Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is increasingly used to detect changes in posttranslational modifications (PTMs) in samples from different conditions. Analysis of data from such experiments faces numerous statistical challenges. These include the low abundance of modified proteoforms, the small number of observed peptides that span modification sites, and confounding between changes in the abundance of PTM and the overall changes in the protein abundance. Therefore, statistical approaches for detecting differential PTM abundance must integrate all the available information pertaining to a PTM site and consider all the relevant sources of confounding and variation. In this manuscript, we propose such a statistical framework, which i

SUBMITTER: Kohler D 

PROVIDER: S-EPMC9860394 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature