The invention provides reagents, methods, and compositions for studying protein-protein interactions. The inventive system and methods allow the analysis of protein-protein interactions in vivo and in vitro. Advantages offered by various embodiments of the inventive system and methods compared to existing photocrosslinking approaches include, for example, (i) novel reversible crosslinking reagents that allow easy isolation, purification, and enrichment of the crosslinked products; (ii) trifiuoromethyl phenyldiazirine- or perfluorinaled phenylazide-based photocrosslinking reagents that provide high specific labeling, no side product, and higher photocrosslinking efficiency; (iii) versatile spacer groups that allow systematic contact site mapping; (iv) novel methods for isolating, purifying, and detecting crosslinked products based on the reversible-link chemistry; and (v) the ability to study the interaction sites in vitro, in situ, or in vivo.
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