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Collins M.O., Husi H., Yu L., Brandon J.M., Anderson C.N., Blackstock W.P., Choudhary J.S., and Grant S.G. Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome. J Neurochem 97 Supp1 (2006) 16-23. This mass spectrometry-based study determined the in vivo protein composition of membrane-associated signaling complexes of the post-synaptic density region of synapses. This study provides very useful information to disentangle tissue-specific networks (e.g. for neurons) form large interaction maps.
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Uhlen M., Bjorling E., Agaton C., Szigyarto C.A., Amini B., Andersen E., Andersson A.C., Angelidou P., Asplund A., Asplund C., et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4 (2005) 1920-1932. This study presents a human protein atlas based on tissue staining with over 700 different antibodies. It gives a nice account on different methods to validate antibodies. Projects devoted to the systematic generation of antibodies might become equally important tools for the mass spectrometry-based complex purification approaches as the ORFeome projects are for systematic Y2H analysis.
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The paper is an updated report on the human protein reference database (HPRD), including a network analysis of the more than 25 000 interactions that have been collected from the literature. The HPRD dataset, not only because of its size but also because of its 'puristic' approach to collect literature data, is a very useful benchmark for the analysis of other systematically generated data.
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Ramani A.K., Bunescu R.C., Mooney R.J., and Marcotte E.M. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 6 (2005) R40
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As a result of a collaborative research program, the authors show that integration of a protein-interaction network (generated by a text mining approach) with expression profiling data can indeed lead to network states reflecting dynamic cellular processes. Addressing endotoxin-stimulated inflammation in blood leukocytes, it is one of the first reports generating disease relevant network states for human.
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Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone
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This study describes a large set of yeast Hsp90 interacting proteins, combining four different screening approaches. It shows that each approach provides biologically meaningful information, even if the results of individual approaches show little overlap.
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Zhao R., Davey M., Hsu Y.C., Kaplanek P., Tong A., Parsons A.B., Krogan N., Cagney G., Mai D., Greenblatt J., et al. Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell 120 (2005) 715-727. This study describes a large set of yeast Hsp90 interacting proteins, combining four different screening approaches. It shows that each approach provides biologically meaningful information, even if the results of individual approaches show little overlap.
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