Generating and navigating proteome maps using mass spectrometry

Complete proteome reference maps, which contain validated, mass spectrometry (MS)-derived, reference fragment ion spectra for unique peptides for each protein of a proteome, are becoming an indispensible resource to quantify the dynamic behaviour of a proteome, or subsets thereof, under multiple conditions.Despite enormous technical advances in shotgun proteomics, which is the main MS-based proteome technology today, the generation of such reference maps has been challenging and expensive.The use of synthetic peptide libraries representing unique peptides for each protein of a proteome, and the fragment ion spectra derived from these compounds, are a good basis for the generation of complete proteome reference maps.To generate and use proteome reference maps, the precise level of resolution of proteome analysis needs to be considered and carefully defined. Specifically, resolving splice forms or differentially modified proteins poses different challenges compared to the quantification of the primary translation products of a gene locus.New MS techniques that use proteome reference maps as prior information support the quantification of complete or partial proteomes at unprecedented levels of reproducibility, sensitivity and dynamic range. Reminiscent of microarray-based gene expression analysis, such capabilities will allow the quantitative monitoring of dynamic protein expression in different cells and tissues at different states, and are particularly important for systems biology and clinical research.Proteomics is moving from an era focused on the perpetual discovery of proteins towards an era of determining the relevant biological information about proteins. Complete proteome maps will be an essential element to realize this fundamental transition.