Traveling-Wave Ion Mobility Mass Spectrometry Analysis of Isomeric Modified Peptides Arising from Chemical Cross-Linking

Traveling-wave ion mobility (TWIM) coupled to mass spectrometry (MS) has emerged as a powerful tool for structural and conformational analysis of proteins and peptides, allowing the analysis of isomeric peptides (or proteins) with the same sequence but modified at different residues This work demonstrates the use of the novel TWIM-MS technique to separate isomeric peptide ions derived from chemical cross-linking experiments, which enables the acquisition of distinct product ion spectra for each isomer, clearly indicating modification on different sites Experiments were performed with four synthetic peptides, for which variable degrees of mobility separation were achieved In cases of partially overlapping mobility arrival time distributions (ATDs), extracting the ATDs of fragment ions belonging to each individual isomer allowed their separation into two distinct ATDs Accumulation over regions from the specific ATDs generates the product ion spectrum of each isomer, or a spectrum highly enriched in their fragments The population of both modified peptide isomers was correlated with the intrinsic reactivities of different Lys residues from reactions conducted at different pH conditions (J Am Soc Mass Spectrom 2010, 21, 2062-2069) (C) 2010 Published by Elsevier Inc on behalf of American Society for Mass Spectrometry