Document Detail


STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.
MedLine Citation:
PMID:  23303698     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.
Authors:
Paul D Piehowski; Vladislav A Petyuk; John D Sandoval; Kristin E Burnum; Gary R Kiebel; Matthew E Monroe; Gordon A Anderson; David G Camp; Richard D Smith
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2013-02-04
Journal Detail:
Title:  Proteomics     Volume:  13     ISSN:  1615-9861     ISO Abbreviation:  Proteomics     Publication Date:  2013 Mar 
Date Detail:
Created Date:  2013-03-08     Completed Date:  2013-08-26     Revised Date:  2014-03-03    
Medline Journal Info:
Nlm Unique ID:  101092707     Medline TA:  Proteomics     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  766-70     Citation Subset:  IM    
Copyright Information:
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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MeSH Terms
Descriptor/Qualifier:
Bacterial Proteins / analysis,  chemistry
Blood Proteins / analysis,  chemistry
Databases, Protein*
Humans
Peptide Fragments / analysis,  chemistry*
Proteins / analysis,  chemistry*
Proteomics / methods*
Shewanella
Tandem Mass Spectrometry / methods*
Grant Support
ID/Acronym/Agency:
P01 DA026134/DA/NIDA NIH HHS; P01 DA026134/DA/NIDA NIH HHS; P41 RR018522/RR/NCRR NIH HHS; RR018522/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Bacterial Proteins; 0/Blood Proteins; 0/Peptide Fragments; 0/Proteins
Comments/Corrections

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


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