Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics

This chapter outlines general principals that apply to the analysis of posttranslational modifications of proteins, with an emphasis on phosphoproteins. Mass spectrometry (MS)-based approaches for selective detection and site-specific analysis of posttranslationally modified peptides are described, and an MS-based method that relies on production and detection of fragment ions specific for the modification(s) of interest and that was developed in the authors' laboratory is described in detail. The method is applicable to selective detection of N- and O-linked carbohydrates in glycoproteins, O-linked sulfate, and N- and O-linked lipids. Detailed procedures for application of this strategy to phosphorylation-site mapping are presented here.