In MS2_MS3 experiments, the crosslinked peptide is first fragmented into single peptides by breaking the crosslinker. The peptide fragments are isolated from the MS2 scan and fragmented as single peptides in the MS3 spectra. All four MS3 spectra of the crosslinked peptides contain only a single peptide that is specified in the label on top of the spectrum as shown in the following figure.

Crosslinking peptides identified by MS2 spectral scan