deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS

Abstract

Characterization of protein structural changes in response to protein modifications, ligand or chemical binding, or protein-protein interactions is essential for understanding protein function and its regulation. Amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is one of the most favorable tools for characterizing the protein dynamics and changes of protein conformation. However, currently the analysis of HDX-MS data is not up to its full power as it still requires manual validation by mass spectrometry experts. Especially, with the advent of high throughput technologies, the data size grows everyday and an automated tool is essential for the analysis. Here, we introduce a fully automated software, referred to as 'deMix', for the HDX-MS data analysis. deMix deals directly with the deuterated isotopic distributions, but not considering their centroid masses and is designed to be robust over random noises. In addition, unlike the existing approaches that can only determine a single state from an isotopic distribution, deMix can also detect a bimodal deuterated distribution, arising from EX1 behavior or heterogeneous peptides in conformational isomer proteins. Furthermore, deMix comes with visualization software to facilitate validation and representation of the analysis results.