Identification of post-translational modifications via blind search of mass-spectra

Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

25 Scopus citations

Abstract

Post-translational modifications (PTMs) are of great biological importance. Most existing approaches perform a restrictive search that can only take into account a few types of PTMs and ignore all others. We describe an unrestrictive PTM search algorithm that searches for all types of PTMs at once in a blind mode, i.e., without knowing which PTMs exist in a sample. The blind PTM identification opens a possibility to study the extent and frequencies of different types of PTMs, still an open problem in proteomics. Using our new algorithm, we were able to construct a two-dimensional PTM frequency matrix that reflects the number of MS/MS spectra in a sample for each putative PTM type and each amino acid. Application of this approach to a large IKKb dataset resulted in the largest set of PTMs reported for a single MS/MS sample so far. We demonstrate an excellent correlation between high values in the PTM frequency matrix and known PTMs thus validating our approach. We further argue that the PTM frequency matrix may reveal some still unknown modifications that warrant further experimental validation.

Original languageEnglish
Title of host publicationProceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
Pages157-166
Number of pages10
DOIs
StatePublished - 1 Dec 2005
Externally publishedYes
Event2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 - Stanford, CA, United States
Duration: 8 Aug 200511 Aug 2005

Publication series

NameProceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Volume2005

Conference

Conference2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Country/TerritoryUnited States
CityStanford, CA
Period8/08/0511/08/05

ASJC Scopus subject areas

  • General Engineering
  • General Medicine

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