TY - JOUR
T1 - Testing and Validation of Computational Methods for Mass Spectrometry
AU - Gatto, Laurent
AU - Hansen, Kasper D.
AU - Hoopmann, Michael R.
AU - Hermjakob, Henning
AU - Kohlbacher, Oliver
AU - Beyer, Andreas
N1 - Publisher Copyright:
© 2015 American Chemical Society.
PY - 2016/3/4
Y1 - 2016/3/4
N2 - 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.
AB - 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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U2 - 10.1021/acs.jproteome.5b00852
DO - 10.1021/acs.jproteome.5b00852
M3 - Article
C2 - 26549429
AN - SCOPUS:84960364338
SN - 1535-3893
VL - 15
SP - 809
EP - 814
JO - Journal of proteome research
JF - Journal of proteome research
IS - 3
ER -