Testing and Validation of Computational Methods for Mass Spectrometry

Laurent Gatto, Kasper D. Hansen, Michael R. Hoopmann, Henning Hermjakob, Oliver Kohlbacher, Andreas Beyer

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)809-814
Number of pages6
JournalJournal of proteome research
Issue number3
StatePublished - Mar 4 2016

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


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