PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features.

Autor:	Schwämmle V; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark. Electronic address: veits@bmb.sdu.dk., Hagensen CE; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark., Rogowska-Wrzesinska A; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark., Jensen ON; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
Jazyk:	angličtina
Zdroj:	Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2020 Aug; Vol. 19 (8), pp. 1396-1408. Date of Electronic Publication: 2020 May 18.
DOI:	10.1074/mcp.RA119.001777
Abstrakt:	Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be sufficiently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across different biological samples due to ubiquitous missing values. A robust statistical test provides accurate confidence scores of large-scale proteomics results, regardless of instrument platform, experimental protocol and software tools. However, the multitude of different combinations of experimental strategies, mass spectrometry techniques and informatics methods complicate the decision of choosing appropriate statistical approaches. We address this challenge by introducing PolySTest, a user-friendly web service for statistical testing, data browsing and data visualization. We introduce a new method, Miss test, that simultaneously tests for missingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. We demonstrate that PolySTest with integrated Miss test achieves higher confidence and higher sensitivity for artificial and experimental proteomics data sets with known ground truth. Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from differentiating muscle cells resulted in the rescue of 10-20% additional proteins in the identified molecular networks relevant to muscle differentiation. We conclude that PolySTest is a valuable addition to existing tools and instrument enhancements that improve coverage and depth of large-scale proteomics experiments. A fully functional demo version of PolySTest and Miss test is available via http://computproteomics.bmb.sdu.dk/Apps/PolySTest. Competing Interests: Conflict of interest—No author has an actual or perceived conflict of interest with the contents of this article. (© 2020 Schwämmle et al.)
Databáze:	MEDLINE
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