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

By M. Gstaiger, R. Aebersold. Nature reviews genetics, 2009

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A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “This has enabled many powerful proteomic applications, including global analysis of post-translational modifications [3], large-scale reconstruction of protein interaction networks [4], and deep quantitative proteome profiling of model organisms [5].”
A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction (2011, background): “Large protein-protein interaction (PPI) networks can be generated by systematic yeast two-hybrid (Y2H) studies ( 9 ) or protein complex isolation and mass spectrometry approaches ( 10 ).”
Visualization of omics data for systems biology (2010, background): “, a promising emerging technology is quantitative protein expression profiling based on mass spectrometr”