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  Testing and Validation of Computational Methods for Mass Spectrometry

Gatto, L., Hansen, K., Hoopmann, M., Hermjakob, H., & Kohlbacher, O. (2016). Testing and Validation of Computational Methods for Mass Spectrometry. Journal of Proteome Research, 15(3), 809-814. doi:10.1021/acs.jproteome.5b00852.

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 Creators:
Gatto, L, Author
Hansen, KD, Author
Hoopmann, MR, Author
Hermjakob, H, Author
Kohlbacher, O1, Author           
Affiliations:
1Research Group Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3380092              

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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.

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 Dates: 2016-03
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1021/acs.jproteome.5b00852
PMID: 26549429
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Title: Journal of Proteome Research
  Other : J. Proteome Res.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 15 (3) Sequence Number: - Start / End Page: 809 - 814 Identifier: ISSN: 1535-3893
CoNE: https://pure.mpg.de/cone/journals/resource/111019664290000