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

D. Tsur, S. Tanner, E. Zandi, V. Bafna, P.A. Pevzner
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
While identifying post-translational modifications (PTMs) is undoubtedly the next big step for proteomics, most MS/MS database search algorithms 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 (MS-Alignment ) that searches for all types of PTMs at once in a blind mode, i.e., without knowing which PTMs exist in nature. The blind PTM identification opens a possibility to study the extent and
more » ... requency of different types of PTMs, still an open problem in proteomics. We use MS-Alignment 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 lens proteins resulted in a largest set of PTMs reported in human crystallins so far. Our analysis of various MS/MS datasets implies that the biological phenomenon of modification is much more widespread than previously thought. We further argue that MS-Alignment reveals some still unknown types of modifications that warrant further experimental validation.
doi:10.1109/csb.2005.34 dblp:conf/csb/TsurTZBP05 fatcat:3m6nz3wmqzaedd2y7deftnhcju