Project description:Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful protein footprinting technique to study protein dynamics and binding; however, HDX-MS data analysis is often challenging and time consuming. Moreover, the HDX community is expanding to investigate multi-protein and highly complex protein systems such as cell lysates which further complicates data analysis. Thus, a simple and easy-to-use open source software package designed to analyze large and highly complex protein systems is needed. In this vein, we have developed The Deuterium Calculator, a Python-based software package for HDX-MS data analysis. The Deuterium Calculator is capable of differential and nondifferential HDX-MS analysis, produces standardized data files according to the recommendations put forth by the International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX) to increase transparency in data analysis, and generates Woods’ plots for statistical analysis and data visualization. This standard output can be used to perform further analysis on HDX such as determination of labeling time dependent deuteration and for the study of protein folding kinetics or differential uptake. Moreover, the Deuterium Calculator is capable of analyzing large HDX-MS datasets (e.g., LC-HDX-MS from complex samples such as cell lysates) to determine the extent of deuteration on individual peptides from numerous proteins, perform differential analysis under varying experimental conditions, and time-dependent deuterium exchange. The Deuterium Calculator is freely available for download at https://github.com/OUWuLab/TheDeuteriumCalculator.git.
Project description:We employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the conformational dynamics required to facilitate based Brownian ratchet mechanism for protein secretion (by the SecA-SecYEG complex).
Project description:Hydrogen deuterium exchange mass spectrometry of HSL in the presence of artificial lipid droplets to analyze lipid droplets binding.
Project description:Hydrogen deuterium exchange mass spectrometry of PLIN3 in the presence of three different membrane vesicles to analyze structural changes induced by membrane binding.
Project description:Hydrogen deuterium exchange mass spectrometry (HDX-MS) is widely used for epitope analysis of the antibod-ies. However, epitope analysis of glycoproteins is challenging because of the heterogeneity of attached N-linked glycans. Recent studies have reported methods where N-linked glycans were removed at low pH follow-ing hydrogen deuterium exchange reactions, but the methods for glycoproteins remain controversial. Here, we demonstrate the utility of using antigens with uniformed N-linked glycans in glycoprotein epitope analysis by HDX-MS. By treating HEK293 cells with kifunensine, we were able to prepare antigens mainly with N-linked high-mannose-type glycans. Analysis of epitopes of a monoclonal antibody S309 using antigens prepared with this method allowed us to identify an epitope that included the previously reported N-linked glycan attachment sites for this antibody. We propose that using antigens with uniformed glycans should be effective for epitope analysis of glycoproteins, such as virus spike proteins covered by glycan shields. Moreover, we believe that this approach accelerates research on vaccines and neutralizing antibodies against viruses that escape host immunity through glycan shields or mutations.