Applying mass spectrometry-based proteomics to genetics, genomics and network biology

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Abstract
Mass spectrometry-based proteomics is the only method currently available to comprehensively analyse changes in mutant proteomes. Several quantitative methods have been introduced to profile mutant proteomes with high sensitivity. However, although full proteome coverage has been achieved by recent studies, proteome profiling still requires substantial experimental efforts. Targeted proteome analysis by selected reaction monitoring is a promising analytical concept to overcome the existing limitations in the analysis of low abundance proteins from complex biological samples. Several workflows have been introduced for the systematic analysis of posttranslational modifications. The first examples in the field of phosphoproteome analysis have shown how global posttranslational modification profiling can be applied to identify the molecular pathways that are affected in mutant cells. Information on protein complexes obtained by affinity purification coupled with mass spectrometry provides important insights into the molecular context of proteins that are encoded by mutated genes. A higher-level understanding of complex genotype–phenotype relationships will depend on the proper annotation and accessibility of mass spectrometry-based proteomics data to integrate these data with functional genomics and phenomics data in a biological cyberinfrastructure.