Enhancing Cysteine Chemoproteomic Coverage Through Systematic Assessment of Click Chemistry Product Fragmentation

Higher-energy C-trap dissociation (HCD) of triazole-and biotin-modified peptides affords several characteristic fragment ions, including previously reported and newly identified species. Using the open and mass offset search strategies, we conduct an in-depth analysis of the relative intensities and specificity of these signature fragments. Through comparison of structurally matched isotopologues, we pinpoint the nature of the observed fragments.By varying the nature of the labeling reagent, including linker length, number of fragmentable bonds, and position of the triazole, we also achieve improved coverage of labeled peptides. The combination of labile and non-labile ion searches also affords an improvement in the chemoproteomic detected (CpD) cysteines identified. Collectively our study demonstrates the utility of labile ion and mass offset search strategies in the analysis of chemoproteomics datasets and reveals the ubiquity of triazole fragmentation in MS/MS analysis of chemically modified peptides.