Light-Induced Orthogonal Fragmentation of Crosslinked Peptides

Crosslinking mass spectrometry provides pivotal informationonthe structure and interaction of proteins. MS-cleavable crosslinkersare regarded as a cornerstone for the analysis of complex mixtures.Yet they fragment under similar conditions as peptides, leading tomixed fragmentation spectra of the crosslinker and peptide. This hampersselecting individual peptides for their independent identification.Here, we introduce orthogonal cleavage using ultraviolet photodissociation(UVPD) to increase crosslinker over peptide fragmentation. We designedand synthesized a crosslinker that can be cleaved at 213 nm in a commercialmass spectrometer configuration. In an analysis of crosslinked Escherichia coli lysate, the crosslinker-to-peptidefragment intensity ratio increases from nearly 1 for a conventionallycleavable crosslinker to 5 for the UVPD-cleavable crosslinker. Thislargely increased the sensitivity of selecting the individual peptidesfor MS3, even more so with an improved doublet detection algorithm.Data are available via ProteomeXchange with identifier PXD040267.

Automated summary

Crosslinking mass spectrometry is important for studying the structure and interaction of proteins. We have introduced orthogonal cleavage using ultraviolet photodissociation (UVPD) to increase the fragmentation of crosslinkers relative to peptides, which improves the selectivity for identifying individual peptides. By using this method, the crosslinker-to-peptide fragment intensity ratio increased from nearly 1 for a conventionally cleavable crosslinker to 5 for the UVPD-cleavable crosslinker in an analysis of crosslinked Escherichia coli lysate. This greatly enhanced the sensitivity for selecting individual peptides.