Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes

Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.