Proteomics by mass spectrometry—Go big or go home?

Mass spectrometry is an important technology for mapping composition and flux in whole proteomes. Over the last 5 years in particular, impressive gains in the depth of proteome coverage have been realized, particularly for model organisms. This review will provide an update on advancements in the key analytical techniques, methods and informatics directed towards whole proteome analysis by mass spectrometry. Practical issues involving sample requirements, analysis time and depth of coverage will be addressed, to gauge how useful data-driven approaches are for solving biological problems. Targeted mass spectrometric methods, based on selected reaction monitoring, are presented as a powerful alternative to data-driven methods. They offer robust, transferable protocols for hypothesis-directed monitoring of limited yet biologically significant tracts of any proteome.