Literature DB >> 30560673

Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate.

Uri Keich1, Kaipo Tamura2, William Stafford Noble2,3.   

Abstract

Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed data set analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, data sets, or databases. The average TDC (aTDC) protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.

Entities:  

Keywords:  false discovery rate; mass spectrometry; spectrum identification

Mesh：

Year:  2019        PMID： 30560673      PMCID： PMC6919216          DOI： 10.1021/acs.jproteome.8b00802

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  23 in total

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Authors:  David Fenyö; Ronald C Beavis
Journal:  Anal Chem       Date:  2003-02-15       Impact factor: 6.986

2.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

3.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors:  Joshua E Elias; Steven P Gygi
Journal:  Nat Methods       Date:  2007-03       Impact factor: 28.547

4.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

Authors:  J K Eng; A L McCormack; J R Yates
Journal:  J Am Soc Mass Spectrom       Date:  1994-11       Impact factor: 3.109

5.  Computing exact p-values for a cross-correlation shotgun proteomics score function.

Authors:  J Jeffry Howbert; William Stafford Noble
Journal:  Mol Cell Proteomics       Date:  2014-06-02       Impact factor: 5.911

6.  Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach.

Authors:  Lev I Levitsky; Mark V Ivanov; Anna A Lobas; Mikhail V Gorshkov
Journal:  J Proteome Res       Date:  2016-12-13       Impact factor: 4.466

Review 7.  Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

Authors:  Kenneth Verheggen; Helge Raeder; Frode S Berven; Lennart Martens; Harald Barsnes; Marc Vaudel
Journal:  Mass Spectrom Rev       Date:  2017-09-13       Impact factor: 10.946

8.  Faster SEQUEST searching for peptide identification from tandem mass spectra.

Authors:  Benjamin J Diament; William Stafford Noble
Journal:  J Proteome Res       Date:  2011-07-29       Impact factor: 4.466

9.  Statistical calibration of the SEQUEST XCorr function.

Authors:  Aaron A Klammer; Christopher Y Park; William Stafford Noble
Journal:  J Proteome Res       Date:  2009-04       Impact factor: 4.466

10.  Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.

Authors:  Sangtae Kim; Nitin Gupta; Pavel A Pevzner
Journal:  J Proteome Res       Date:  2008-07-03       Impact factor: 4.466
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  4 in total

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Authors:  Zach Rolfs; Lloyd M Smith
Journal:  J Proteome Res       Date:  2021-11-05       Impact factor: 4.466

2.  An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.

Authors:  Laura Fancello; Thomas Burger
Journal:  Genome Biol       Date:  2022-06-20       Impact factor: 17.906

3.  Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.

Authors:  Andy Lin; Deanna L Plubell; Uri Keich; William S Noble
Journal:  J Proteome Res       Date:  2021-07-08       Impact factor: 5.370

4.  Null-free False Discovery Rate Control Using Decoy Permutations.

Authors:  Kun He; Meng-Jie Li; Yan Fu; Fu-Zhou Gong; Xiao-Ming Sun
Journal:  Acta Math Appl Sin       Date:  2022-04-09       Impact factor: 1.102
  4 in total

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