Accurate annotation of peptide modifications through unrestrictive database search.

TitleAccurate annotation of peptide modifications through unrestrictive database search.
Publication TypeJournal Article
Year of Publication2008
AuthorsTanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V
JournalJ Proteome Res
Date Published2008 Jan
KeywordsDatabases, Protein, Information Storage and Retrieval, Peptides, Polymorphism, Genetic, Protein Processing, Post-Translational, Proteins, Software, Tandem Mass Spectrometry

Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.

PubMed URL
Alternate TitleJ. Proteome Res.
PubMed ID18034453