Analysis of Mass Spectrometry data: Significance Analysis of Microarrays for SELDI-MS Data in Proteomics

Abstract

Mass Spectrometry (MS) has arguably become thecore technology in proteomics. MALDI and SELDI-TOFtechniques enable the study biological fluids, e.g. human blood.Analysis of these samples can lead to discover new biomarkerswhich can ease the diagnostic and prognostic of several diseases,e.g. various cancers. In this work, we focus on MS data fromSELDI-TOF experiments. We begin with a preprocessing step inorder to remove noises due to the acquisition process of the data.Then, we apply the differential analysis to a SELDI-MS data,using the Significance Analysis of Microarray (SAM) methodimplemented in Matlab. Results using the SAM method arecompared with those obtained by the conventional t-test andAnalysis Of Variance (ANOVA) in order to evaluate its efficacyand its performance. As a result, we demonstrate that the SAMmethod can be adapted for effective significance analysis ofSELDI-MS data. It is deemed powerful and provides betterresults that totes. An easy-to-use application is developed withMatlab for mass spectrometry data analysis from raw spectra todifferential analysis, including the SAM method