Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociation

Further improving the proteomic identification coverage and reliability is still challenging in the mass spectrometry (MS)-based proteomics. Herein, we combine VAILase and trypsin digestion with 193-nm ultraviolet photodissociation (UVPD) and higher-energy collision dissociation (HCD) to improve the performance of bottom-up proteomics. As VAILase exhibits high complementarity to trypsin, the proteome sequence coverage is improved obviously whether with HCD or 193-nm UVPD. The high diversity of fragment ion types produced by UVPD contributes to the improvements of identification reliability for both trypsin-and VAILase-digested peptides with an average XCorr score improvement of 10%. ? 2021 Elsevier B.V. All rights reserved.

Automated summary

The combination of VAILase and trypsin digestion with 193-nm UVPD and HCD improves the performance of bottom-up proteomics by enhancing proteome sequence coverage and identification reliability. UVPD generates a high diversity of fragment ion types, contributing to a significant improvement in the XCorr score for both trypsin- and VAILase-digested peptides.