Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions.
The past 10 years have witnessed a dramatic proliferation in the availability of protein interaction data. However, for interaction mapping based on affinity purification coupled with mass spectrometry (AP-MS), there is a wealth of information present in the datasets that often goes unrecorded in public repositories, and as such remains largely unexplored. Further, how this type of data is represented and used by bioinformaticians has not been well established. Here, we point out some common mistakes in how AP-MS data are handled, and describe how protein complex organization and interaction dynamics can be inferred using quantitative AP-MS approaches.
Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Canada. gingras@lunenfeld.ca
Anne-Claude
AC
Gingras
Brian
B
Raught
D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008954:Models, Biological; D016366:Open Reading Frames; D010455:Peptides / Q000737:chemistry; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D012984:Software
D018076:DNA, Complementary; D010455:Peptides; D011506:Proteins