Identification of post-translational modifications by blind search of mass spectra.

TitleIdentification of post-translational modifications by blind search of mass spectra.
Publication TypeJournal Article
Year of Publication2005
AuthorsTsur D, Tanner S, Zandi E, Bafna V, Pevzner PA
JournalNat Biotechnol
Date Published2005 Dec
KeywordsAlgorithms, Amino Acid Sequence, Artificial Intelligence, Crystallins, Lens, Crystalline, Mass Spectrometry, Molecular Sequence Data, Pattern Recognition, Automated, Peptide Mapping, Protein Processing, Post-Translational, Proteome, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid

Most tandem mass spectrometry (MS/MS) database search algorithms perform a restrictive search that takes into account only a few types of post-translational modifications (PTMs) and ignores all others. We describe an unrestrictive PTM search algorithm, MS-Alignment, that searches for all types of PTMs at once in a blind mode, that is, without knowing which PTMs exist in nature. Blind PTM identification makes it possible to study the extent and frequency of different types of PTMs, still an open problem in proteomics. Application of this approach to lens proteins resulted in the largest set of PTMs reported in human crystallins so far. Our analysis of various MS/MS data sets implies that the biological phenomenon of modification is much more widespread than previously thought. We also argue that MS-Alignment reveals some uncharacterized modifications that warrant further experimental validation.

PubMed URL
Alternate TitleNat. Biotechnol.
PubMed ID16311586