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Exhaustive Database Searching for Amino Acid Mutations in Proteomes.
MedLine Citation:
PMID:  22581177     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
MOTIVATION: Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing. RESULTS: The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on bench-marking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage. AVAILABILITY: The Sipros algorithm is freely available at http://code.google.com/p/sipros. CONTACT: panc@ornl.gov.
Authors:
Doug Hyatt; Chongle Pan
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-5-10
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  -     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-5-14     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
BioSciences Division and Computer Science and Mathematics Division, Oak Ridge National Laboratory.
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