Cleavable Cross-Linkers Redefined by a Novel MS3-Trigger Algorithm

Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a MS3-based approach for identifying cross-linked peptides. However, MS2 (MS/MS)-based approaches currently outperform approaches utilizing MS3. We show here that the sensitivity and specificity of triggering MS3 have been hampered algorithmically. Our four-step MS3-trigger algorithm greatly outperformed currently employed methods and comes close to reaching the theoretical limit.

Automated summary

Cross-linking mass spectrometry is transitioning to enable structural systems biology, with MS3-based approaches for identifying cross-linked peptides showing potential despite MS2-based methods currently outperforming.