A Workflow for Large Scale Detection and Validation of Peptide Modifications by RPLC-LTQ-Orbitrap; application to the Arabidopsis thaliana leaf proteome and an on-line modified peptide library

摘要

We describe a workflow for the processing of the large-scale tandem MS datasets, which includes peptide modification and retention time analysis. Except for Mascot, this workflow uses no additional commercial software, and can be easily implemented on a variety of mass spectrometry-based proteomics platforms. The presented PTM-mining method allows for rapid assessment of peptide heterogeneity in tandem MS data, including both physiologically-induced PTMs, non-physiological modifications, and amino acid substitutions and can provide PM-related corrections for label-free and stable-isotope based quantifications. The modification data for the Arabidopsis leaf proteome is accessible online via the Plant Proteomics Database, PPDB.