Universität zu Köln

Gatto, Laurent ORCID: 0000-0002-1520-2268, Hansen, Kasper D., Hoopmann, Michael R., Hermjakob, Henning ORCID: 0000-0001-8479-0262, Kohlbacher, Oliver and Beyer, Andreas ORCID: 0000-0002-3891-2123 (2016). Testing and Validation of Computational Methods for Mass Spectrometry. J. Proteome Res., 15 (3). S. 809 - 815. WASHINGTON: AMER CHEMICAL SOC. ISSN 1535-3907

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Abstract

High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets (http://compms.org/ RefData) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Gatto, Laurent UNSPECIFIED orcid.org/0000-0002-1520-2268 UNSPECIFIED Hansen, Kasper D. UNSPECIFIED UNSPECIFIED UNSPECIFIED Hoopmann, Michael R. UNSPECIFIED UNSPECIFIED UNSPECIFIED Hermjakob, Henning UNSPECIFIED orcid.org/0000-0001-8479-0262 UNSPECIFIED Kohlbacher, Oliver UNSPECIFIED UNSPECIFIED UNSPECIFIED Beyer, Andreas UNSPECIFIED orcid.org/0000-0002-3891-2123 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-283888
DOI:	10.1021/acs.jproteome.5b00852
Journal or Publication Title:	J. Proteome Res.
Volume:	15
Number:	3
Page Range:	S. 809 - 815
Date:	2016
Publisher:	AMER CHEMICAL SOC
Place of Publication:	WASHINGTON
ISSN:	1535-3907
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RNA-SEQ; REAL DATA; SIMULATION; DISCOVERY; ABUNDANCE; SOFTWARE; TOOLS Multiple languages Biochemical Research Methods Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/28388