Fig. 2.

Experimental scheme. A, Sample preparation scheme for cross-linking experiments. B, Demonstration of LC-MS experiment with alternating In Source Collision Induced Dissociation (ISCID) voltage settings. The cross-linked complexes remain intact in the precursor scan (ISCID voltage 0V). ISCID scan at 80V results in cleavage of the labile bonds in the cross-linker and release of reporter and peptides. Cross-linked pairs were identified by searching for PIR mass relationships. C, A separate LC-MS/MS experiment was used to target released peptides for MS/MS analysis at specific mass and retention times. Database search with Mascot was used to identify their sequences of released peptides.