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Mass spectrometrists should search for all peptides, but assess only the ones they care about

View ORCID ProfileAdriaan Sticker, View ORCID ProfileLennart Martens, Lieven Clement
doi: https://doi.org/10.1101/094581
Adriaan Sticker
1Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Belgium
2Medical Biotechnology Center, VIB, Ghent, Belgium
3Department of Biochemistry, Ghent University, Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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  • ORCID record for Adriaan Sticker
Lennart Martens
2Medical Biotechnology Center, VIB, Ghent, Belgium
3Department of Biochemistry, Ghent University, Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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  • For correspondence: lennart.martens@vib-ugent.be lieven.clement@ugent.be
Lieven Clement
1Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Belgium
4Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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  • For correspondence: lennart.martens@vib-ugent.be lieven.clement@ugent.be
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Abstract

In shotgun proteomics identified mass spectra that are deemed irrelevant to the scientific hypothesis are often discarded. Noble (2015)1 therefore urged researchers to remove irrelevant peptides from the database prior to searching to improve statistical power. We here however, argue that both the classical as well as Noble’s revised method produce suboptimal peptide identifications and have problems in controlling the false discovery rate (FDR). Instead, we show that searching for all expected peptides, and removing irrelevant peptides prior to FDR calculation results in more reliable identifications at controlled FDR level than the classical strategy that discards irrelevant peptides post FDR calculation, or than Noble’s strategy that discards irrelevant peptides prior to searching.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 21, 2017.
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Mass spectrometrists should search for all peptides, but assess only the ones they care about
Adriaan Sticker, Lennart Martens, Lieven Clement
bioRxiv 094581; doi: https://doi.org/10.1101/094581
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Mass spectrometrists should search for all peptides, but assess only the ones they care about
Adriaan Sticker, Lennart Martens, Lieven Clement
bioRxiv 094581; doi: https://doi.org/10.1101/094581

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