Document Detail


Identification of post-translational modifications via blind search of mass-spectra.
MedLine Citation:
PMID:  16447973     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Dekel Tsur; Stephen Tanner; Ebrahim Zandi; Vineet Bafna; Pavel A Pevzner
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Publication Detail:
Type:  Evaluation Studies; Journal Article; Research Support, N.I.H., Extramural    
Journal Detail:
Title:  Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference     Volume:  -     ISSN:  1551-7497     ISO Abbreviation:  Proc IEEE Comput Syst Bioinform Conf     Publication Date:  2005  
Date Detail:
Created Date:  2006-02-01     Completed Date:  2007-05-02     Revised Date:  2007-12-03    
Medline Journal Info:
Nlm Unique ID:  101240586     Medline TA:  Proc IEEE Comput Syst Bioinform Conf     Country:  United States    
Other Details:
Languages:  eng     Pagination:  157-66     Citation Subset:  IM    
Affiliation:
Computer Science and Engineering, University of California at San Diego, USA. dtsur@cs.ucsd.edu
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Amino Acid Sequence
Database Management Systems
Databases, Protein*
Information Storage and Retrieval / methods*
Mass Spectrometry / methods*
Molecular Sequence Data
Peptide Mapping / methods*
Protein Processing, Post-Translational*
Proteins / chemistry*
Sequence Alignment / methods
Sequence Analysis, Protein / methods*
Grant Support
ID/Acronym/Agency:
1-R01-RR16522/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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