Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spect

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. Results: In this paper, we describe the first systematic comparison of a wide range of normalisation methods, using two objectives that should be met by a good method. These objectives are minimisation of inter-spectra variance and maximisation of signal with respect to class separation. The fo...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels
• Keywords: Biological Data Analysis, BMCBI 2008, Mass Spectrometry, Normalisation Methods