Document Detail

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.
MedLine Citation:
PMID:  23412978     Owner:  NLM     Status:  MEDLINE    
Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies.
Pratik Jagtap; Jill Goslinga; Joel A Kooren; Thomas McGowan; Matthew S Wroblewski; Sean L Seymour; Timothy J Griffin
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2013-03-15
Journal Detail:
Title:  Proteomics     Volume:  13     ISSN:  1615-9861     ISO Abbreviation:  Proteomics     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-04-12     Completed Date:  2013-09-20     Revised Date:  2014-04-01    
Medline Journal Info:
Nlm Unique ID:  101092707     Medline TA:  Proteomics     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  1352-7     Citation Subset:  IM    
Copyright Information:
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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MeSH Terms
Amino Acid Sequence*
Databases, Protein*
Expressed Sequence Tags
Genomics / methods
Mouth Mucosa / metabolism
Peptides / chemistry*
Proteomics / methods*
Saliva / metabolism
Search Engine*
Sensitivity and Specificity
Tandem Mass Spectrometry / methods
Grant Support
Reg. No./Substance:
Comment In:
Proteomics. 2013 Apr;13(8):1229-30   [PMID:  23504998 ]

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