Data processing and analysis using ProteinChip® data manager software

Mass spectrometry-based clinical proteomics and biomarker research require the processing of large numbers of patient samples in order to attain the statistical significance required to produce robust biomarker candidates. When processed using the high-sensitivity and high-throughput Surface Enhanced Laser Desorption/Ionization ProteinChip SELDI system, the result is an enormous amount of mass spectrometric profiling data. The time and effort required to mine this data and the quality of the candidate biomarkers generated is largely dependent on the quality and appropriate use of the software tools available. This chapter describes the typical workflow for processing and analyzing SELDI data using both univariate and unsupervised multivariate analysis tools.