biostudies-literatureKirsch ZJNational Institutes of HealthNIGMS NIH HHSNIH HHS1030-1039https://www.ebi.ac.uk/biostudies/studies/S-EPMC11167616biostudies-literatureUnknown35(5)Diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) has been extensively utilized to study protein structure and interactions owing to its ease of use, commercial availability, and broad labeling of nucleophilic residues. During typical CL-MS experiments with DEPC, the extent of labeling is kept low to avoid any structural perturbations resulting from covalent modification of the protein. In this study, we demonstrate that proteins can be labeled more extensively via DEPC and still provide accurate structural information. To show this, we modeled labeling kinetics over a range of DEPC concentrations and used molecular dynamics simulations to investigate the molecular-level effects of extensive labeling on the protein structure. Our results indicate that higher extents oJournal of the American Society for Mass SpectrometryProteins Can Withstand More Extensive Labeling while Providing Accurate Structural Information in Covalent Labeling-Mass Spectrometry.PMC11167616S10OD010645R35 GM145272S10 OD010645Kirsch ZJVachet RWfalseProteins Can Withstand More Extensive Labeling while Providing Accurate Structural Information in Covalent Labeling-Mass Spectrometry.Diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) has been extensively utilized to study protein structure and interactions owing to its ease of use, commercial availability, and broad labeling of nucleophilic residues. During typical CL-MS experiments with DEPC, the extent of labeling is kept low to avoid any structural perturbations resulting from covalent modification of the protein. In this study, we demonstrate that proteins can be labeled more extensively via DEPC and still provide accurate structural information. To show this, we modeled labeling kinetics over a range of DEPC concentrations and used molecular dynamics simulations to investigate the molecular-level effects of extensive labeling on the protein structure. Our results indicate that higher extents o2024-01-01T00:00:00Z2024 May2026-06-02T20:44:10.58Z2026-04-20T03:10:36.785ZS-EPMC111676163858147110.1021/jasms.4c00043