MASS SPECTROMETER OUTPUT ANALYSIS TOOL FOR IDENTIFICATION OF PROTEINS

Methods and apparatus for consolidation and visualization of a dataset output from a mass spectrometer. The number of proteins identified in a mass spectrometry experiment may be systematically reduced by identifying and excluding proteins which may not be necessary to explain the observed peptides in a sample. Peptide counts from excluded proteins may be redistributed to non-excluded proteins to preserve total observed peptide counts. The consolidated dataset may be represented as a data structure having a plurality of cells arranged into rows and columns. Visual parameter values may be assigned to various cells in the data structure to emphasize particular features of the data. Data from multiple samples may be arranged in sets of columns in the data structure, and difference scores may be calculated to determine peptide expression differences between the multiples samples. The difference scores may be displayed using textual and/or graphical representations to facilitate data analysis.