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MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics

View ORCID ProfileLudger J.E. Goeminne, Adriaan Sticker, View ORCID ProfileLennart Martens, View ORCID ProfileKris Gevaert, View ORCID ProfileLieven Clement
doi: https://doi.org/10.1101/782466
Ludger J.E. Goeminne
1Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 – S9, B9000 Ghent, Belgium
2VIB-UGent Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
3Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Belgium
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Adriaan Sticker
1Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 – S9, B9000 Ghent, Belgium
2VIB-UGent Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
3Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Belgium
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Lennart Martens
2VIB-UGent Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
3Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Belgium
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Kris Gevaert
2VIB-UGent Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
3Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B9000 Ghent, Belgium
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Lieven Clement
1Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 – S9, B9000 Ghent, Belgium
4Bioinformatics Institute Ghent, Ghent University, Belgium
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  • For correspondence: Lieven.Clement@UGent.be
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ABSTRACT

Missing values are a major issue in quantitative data-dependent mass spectrometry-based proteomics. We therefore present an innovative solution to this key issue by introducing a hurdle model, which is a mixture between a binomial peptide count and a peptide intensity-based model component. It enables dramatically enhanced quantification of proteins with many missing values without having to resort to harmful assumptions for missingness. We demonstrate the superior performance of our method by comparing it with state-of-the-art methods in the field.

Footnotes

  • E-mail: ludger.goeminne{at}UGent.vib.be; adriaan.sticker{at}UGent.vib.be; lennart.martens{at}UGent.vib.be; kris.gevaert{at}UGent.vib.be; lieven.clement{at}UGent.be

  • https://github.com/statOmics/MSqRobHurdlePaper

Copyright 
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-NC 4.0 International license.
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Posted September 25, 2019.
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MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics
Ludger J.E. Goeminne, Adriaan Sticker, Lennart Martens, Kris Gevaert, Lieven Clement
bioRxiv 782466; doi: https://doi.org/10.1101/782466
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MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics
Ludger J.E. Goeminne, Adriaan Sticker, Lennart Martens, Kris Gevaert, Lieven Clement
bioRxiv 782466; doi: https://doi.org/10.1101/782466

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