title: Unrestrictive identification of post-translational modifications through peptide mass spectrometry.
abstract: Proteins are post-translationally modified in vivo as part of cellular regulation and signaling, and undergo further chemical modifications during laboratory processing. Even relatively simple protein samples may carry a wide range of modifications. Peptide tandem mass spectrometry provides a way to study these events. We present a protocol for computational identification of post-translational modifications (PTMs) and the sites where they occur. The protocol performs an unrestrictive search, and requires no prior knowledge of what modifications are present in the sample. We present a largely automated procedure for PTM discovery, and provide a guide for analysis of PTM annotations. This protocol requires you to type out several commands, so you may wish to enlist the help of a colleague familiar with the computer's command-line interface. A typical MS run of up to 25,000 scans can be searched and analyzed in 3 h.
authors.affiliation: Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. stanner@ucsd.edu
authors.forename: Stephen
authors.initials: S
authors.lastname: Tanner
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry*; D011499:Protein Processing, Post-Translational; D012984:Software
chemical_list: D010455:Peptides