Particular aspects provide novel protein interaction reporter (PIR) compounds (e.g., formulas I and II), comprising at least two protein reactive moieties (e.g., N-hydroxysuccinamide), each linked to a reporter moiety (e.g., mass reporter) by a covalent labile bond that is differentially cleavable with respect to peptide bonds (e.g., by a method such as collisional activation in a mass spectrometer, activation by electron capture dissociation (ECD), photoactivation, etc.), wherein the reporter moiety is operatively releasable from the PIR agent upon cleavage of the labile bonds, the released reporter moiety having a characteristic identifying property or label (e.g., m/z value). Particular PIRs comprise a mass reporter moiety, and further comprise an affinity group, (e.g., biotin), linked to the PIR (e.g., to the mass reporter moiety) by a selectively cleavable bone (e.g. photo-labile bond)). Additional aspects provide methods for characterizing intermolecular or intramolecular protein interactions using one or more inventive PIR compounds.
STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH
 This work was supported by U.S. Department of Energy Grant No. DE-FG02-04ER63924, and NIH grant No. S10 RR017805-01. The United States has certain rights in this invention, pursuant to 35 U.S.C. .sctn.202(c)(6).