The identification of the conjugation sites and the studies of protein-protein interactions based on the chemical crosslinking and mass spectrometry share some challenges because both rely on the identification of type 2 peptides. According to a recent collaborative study the automatic assignment of the MS/MS spectra to type 2 peptides although filtered by FDR criteria requires manual inspection even though this process has a subjective nature and it is a time-consuming task. This validation process is mainly based on the sequence coverage observed in the MS/MS spectra for both crosslinked peptides. When this validation process is supported by additional criteria, such as the extracted ion chromatograms , specific isotope labeling at MS level ; and/or other pattern of signals observed in the MS/MS spectra, the output becomes more reliable.