A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis

Chemical cross-linking mass spectrometry (CXMS) has emerged as a powerful technology to analyze protein complexes. However, the progress of in vivo CXMS studies has been limited by cross-linking biocompatibility and data analysis. Herein, a glycosidic bond-based MS-cleavable cross-linker of trehalose disuccinimidyl ester (TDS) was designed and synthesized, which was fragmented in MS under CID/HCD to simplify the cross-linked peptides into conventional single peptides via selective cleavage between glycosidic and peptide bonds under individual MS collision energy. Consequently, the cross-linking identification accuracy and throughput were significantly enhanced, and the popular MS mode of stepped HCD was allowed. In addition, TDS showed proper cell-penetrating properties while being highly water-soluble, making it non-DMSO dependent during solubilization. Collectively, TDS provides a promising toolkit for CXMS characterization of living systems with high biocompatibility and accuracy.

Automated summary

Chemical cross-linking mass spectrometry (CXMS) is a powerful technology for analyzing protein complexes. However, in vivo CXMS studies have been limited by cross-linking biocompatibility and data analysis. In this study, a glycosidic bond-based MS-cleavable cross-linker called trehalose disuccinimidyl ester (TDS) was designed and synthesized, which simplified the cross-linked peptides into conventional single peptides via selective cleavage. TDS showed high biocompatibility and accuracy, enhancing the cross-linking identification accuracy and throughput.