Abstract：
:Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering of peptide or protein identifications. In this work we consider a probability model describing the filtering process and find that, when decoy counting is used for q value estimation and subsequent filtering, a correction has to be introduced into these common equations for TDA-based FDR estimation. We also discuss the scale of variance of false discovery proportion (FDP) and propose using confidence intervals for more conservative FDP estimation in shotgun proteomics. The necessity of both the correction and the use of confidence intervals is especially pronounced when filtering small sets (such as in proteogenomics experiments) and when using very low FDR thresholds.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Levitsky LI,Ivanov MV,Lobas AA,Gorshkov MVdoi
10.1021/acs.jproteome.6b00144subject
Has Abstractpub_date
2017-02-03 00:00:00pages
393-397issue
2eissn
1535-3893issn
1535-3907journal_volume
16pub_type
杂志文章abstract：:Fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. Successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF-MS. Specific identification of the ...
journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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doi：10.1021/acs.jproteome.6b00983
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050415p
更新日期：2006-04-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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journal_title：Journal of proteome research
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doi：10.1021/acs.jproteome.0c00399
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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更新日期：2009-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050298y
更新日期：2006-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00106
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501086e
更新日期：2015-02-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034081k
更新日期：2004-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00373
更新日期：2017-09-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900435z
更新日期：2010-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00345
更新日期：2019-03-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300953k
更新日期：2013-02-01 00:00:00
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journal_title：Journal of proteome research
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更新日期：2012-02-03 00:00:00
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journal_title：Journal of proteome research
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更新日期：2011-02-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00369
更新日期：2016-12-02 00:00:00
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journal_title：Journal of proteome research
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更新日期：2014-11-07 00:00:00
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journal_title：Journal of proteome research
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更新日期：2005-03-01 00:00:00
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
pub_type： 杂志文章
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journal_title：Journal of proteome research
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