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Metabolites 2013, 3(2), 277-293; doi:10.3390/metabo3020277

Peak Detection Method Evaluation for Ion Mobility Spectrometry by Using Machine Learning Approaches

1,2,* , 3
1 Computational Systems Biology Group, Max Planck Institute for Informatics, Saarbrücken, Germany 2 Cluster of Excellence for Multimodal Computing and Interaction. Saarland University,Saarbrücken, Germany 3 Computer Science XI and Collaborative Research Center SFB 876, TU Dortmund, Germany 4 Analytik, BioMedizinZentrum Dortmund, Germany 5 Genome Informatics, Human Genetics, Faculty of Medicine, University of Duisburg-Essen,Essen, Germany 6 Computational Biology Group, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
* Author to whom correspondence should be addressed.
Received: 25 January 2013 / Revised: 15 March 2013 / Accepted: 9 April 2013 / Published: 16 April 2013
(This article belongs to the Special Issue Data Processing in Metabolomics)
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Ion mobility spectrometry with pre-separation by multi-capillary columns (MCC/IMS) has become an established inexpensive, non-invasive bioanalytics technology for detecting volatile organic compounds (VOCs) with various metabolomics applications in medical research. To pave the way for this technology towards daily usage in medical practice, different steps still have to be taken. With respect to modern biomarker research, one of the most important tasks is the automatic classification of patient-specific data sets into different groups, healthy or not, for instance. Although sophisticated machine learning methods exist, an inevitable preprocessing step is reliable and robust peak detection without manual intervention. In this work we evaluate four state-of-the-art approaches for automated IMS-based peak detection: local maxima search, watershed transformation with IPHEx, region-merging with VisualNow, and peak model estimation (PME).We manually generated Metabolites 2013, 3 278 a gold standard with the aid of a domain expert (manual) and compare the performance of the four peak calling methods with respect to two distinct criteria. We first utilize established machine learning methods and systematically study their classification performance based on the four peak detectors’ results. Second, we investigate the classification variance and robustness regarding perturbation and overfitting. Our main finding is that the power of the classification accuracy is almost equally good for all methods, the manually created gold standard as well as the four automatic peak finding methods. In addition, we note that all tools, manual and automatic, are similarly robust against perturbations. However, the classification performance is more robust against overfitting when using the PME as peak calling preprocessor. In summary, we conclude that all methods, though small differences exist, are largely reliable and enable a wide spectrum of real-world biomedical applications.
Keywords: mcc/ims; peak detection; machine learning; ion mobility spectrometry; spectrum analysis mcc/ims; peak detection; machine learning; ion mobility spectrometry; spectrum analysis
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Hauschild, A.-C.; Kopczynski, D.; D'Addario, M.; Baumbach, J.I.; Rahmann, S.; Baumbach, J. Peak Detection Method Evaluation for Ion Mobility Spectrometry by Using Machine Learning Approaches. Metabolites 2013, 3, 277-293.

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