QuiXoT: quantification and statistics of high-throughput proteomics by stable isotope labelling

AbstractIn most software tools for quantification of mass spectrometry-based proteomics by stable isotope labelling (SIL), there is a recurrent disconnection between the use of a statistical model and convenient data visualisation to check correct data modelling. Most of them lack a robust statistical framework, using models which do not account for the major difficulties in proteomics, such as the unbalanced peptide-protein distribution, undersampling, or the correct separation of sources of variance. This makes especially difficult the interpretation of quantitative proteomics experiments. Here we present QuiXoT, an extensively tested quantification and statistics open source software based on a robust and extensively validated statistical model, the WSPP (weighted spectrum, peptide, and protein). Its associated software package allows the user to visually represent and inspect results at all modelled levels (scan, peptide and protein) on routine bases. It is applicable to practically any SIL method (SILAC, iTRAQ, and 18O among others) or MS instrument.