A Strategy for Efficient Identification of Chemically-Crosslinked Sites in Large Protein Complexes Using Label-Free LC-MS/MS Pattern Comparisons and Targeted MS/MS

摘要

Targeted LC-MS/MS analysis of theoretical crosslinks does not increase the number of useful spectra for crosslinked peptides, but some crosslinks are confirmed with higher confidence. Excluding z(velence)2 does not result in the loss of useful data, because the occasional crosslinked peptide observed as a +2 ion is also observed as a +3 ion. The label-free LC-MS/MS pattern comparison approach significantly increases the speed of data interpretation and results in identification of more crosslinks compared with more manual methods or use of several open source MS crosslink analysis programs.