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Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets |
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| Authors: | Wouter Wegdam Perry D Moerland Marrije R Buist Emiel Ver Loren van Themaat Boris Bleijlevens Huub CJ Hoefsloot Chris G de Koster Johannes MFG Aerts |
| Institution: | (1) Department of Gynaecologic Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands;(2) Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands;(3) Clinical Proteomics Group, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands;(4) Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands |
| Abstract: | BackgroundMass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. |
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