Journal
NATURE BIOTECHNOLOGY
Volume 23, Issue 12, Pages 1562-1567Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt1168
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Funding
- NCRR NIH HHS [1-R01-RR16522] Funding Source: Medline
- NEI NIH HHS [EY007755] Funding Source: Medline
- NIGMS NIH HHS [R01GM65325] Funding Source: Medline
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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.
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