Unrestrictive identification of post-translational modifications through peptide mass spectrometry.

TitleUnrestrictive identification of post-translational modifications through peptide mass spectrometry.
Publication TypeJournal Article
Year of Publication2006
AuthorsTanner S, Pevzner PA, Bafna V
JournalNat Protoc
Date Published2006
KeywordsComputational Biology, Databases, Protein, Mass Spectrometry, Peptides, Protein Processing, Post-Translational, Software

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.

PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/17406213?dopt=Abstract
Alternate JournalNat Protoc
PubMed ID17406213