Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic

摘要: Protein phosphorylation is the best-studied posttranslational modification and plays a role in virtually every biological process. Phosphoproteomics analysis of protein on proteome-wide scale, mainly uses same instrumentation analogous strategies as conventional mass spectrometry (MS)-based proteomics. Measurements can be performed either discovery-type, also known shotgun mode, or targeted manner which monitors set priori phosphopeptides, such members signal transduction pathway, across samples. Here, we delineate different experimental levels at measures taken to optimize scope, reliability, information content phosphoproteomic analyses. Various chromatographic chemical protocols exist physically enrich phosphopeptides from proteolytic digests Subsequent spectrometric revolves around peptide ion fragmentation generate sequence identify backbone well phosphate group attachment site(s), modes like collision-induced dissociation (CID), electron transfer (ETD), higher energy collisional (HCD) have been established for phosphopeptide analysis. Computational tools are important identification quantification mapping sites, deposition large-scale phosphoproteome datasets public databases, extraction biologically meaningful by data mining, integration with other types, descriptive predictive modeling. Finally, discuss how orthogonal approaches employed validate newly identified sites biochemical, mechanistic, physiological level. WIREs Dev Biol 2014, 3:83–112. doi: 10.1002/wdev.121 Conflict interest: The author has declared no conflicts interest this article. For further resources related article, please visit website.