Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data |
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| Authors: | Wouter Meuleman Judith YMN Engwegen Marie-Christine W Gast Jos H Beijnen Marcel JT Reinders Lodewyk FA Wessels |
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| Affiliation: | (1) Bioinformatics and Statistics,Department of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands;(2) Information and Communication Theory Group, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands;(3) Department of Pharmacy & Pharmacology, The Netherlands Cancer Institute/Slotervaart Hospital, Amsterdam, The Netherlands |
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| Abstract: | Background Mass spectrometry for biological data analysis is an active field of research, providing an efficient way of high-throughput proteome screening. A popular variant of mass spectrometry is SELDI, which is often used to measure sample populations with the goal of developing (clinical) classifiers. Unfortunately, not only is the data resulting from such measurements quite noisy, variance between replicate measurements of the same sample can be high as well. Normalisation of spectra can greatly reduce the effect of this technical variance and further improve the quality and interpretability of the data. However, it is unclear which normalisation method yields the most informative result. |
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