An isotope labeled asymmetric cross-linker is provided for the detection of cross-linked peptides. A cross-linking and mass spectrometry strategy, referred to as isotope tagging of interacting proteins (iTIP), improves the specificity of detecting cross-linked peptides and accurate identification of the interacting peptide sequences via the incorporation of isotopic signatures that are readily observed in the MS/MS spectrum. Isotope tagged peptides can be identified using mass spectrometry based on doublet peaks in a spectrum. Spectra can be subjected to database search strategies available for the sequencing of linear or non-cross-linked peptides.