Zeitschrift für Proteomik und Bioinformatik
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Crosslinkomics---A New Era of Mapping Protein-Protein Interactions

Jie Luo and Jeff Ranish

A major goal of proteomics is to figure out how proteins interact with one another through networks and within complexes. The development of integrated chemical crosslinking, Mass spectrometric and computation approaches (CXMS) have recently emerged as powerful technologies to study protein interactions and have the potential to significantly advance the field of protein-interaction mapping. The identified crosslinked peptides (two peptides linked by specific crosslinkers), can be used to infer sites of protein-protein interactions and put distance constraints on interacting sites based on the properties of the crosslinkers. Recent reports on the on mapping of interactions within large assemblages such the 15 subunit RNA polymerase II-TFIIF complex [EMBO J 29, 717-726] , the 53 subunit Ribosome[JPR, 10(8):3604-3616] and a partially purified prepartion of the 12 subunit RNA polymerase II [MCP, mcp.M111.008318] suggest that the field of CXMS has matured to the point where its use for mapping protein interactions in large compelxes will soon become more routine. CROSSLINKOMICS, which uses mass spectrometry and computational approaches to identify chemically crosslinked peptides in a high throughput and unbiased manner, is emerging as a new and promising OMICS which has the potential to revolutionize the study of protein-protein interactions.