DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data*

摘要

Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large data sets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculations of relative deuterium uptake into regions of the protein after such corrections, rigorous statistical analysis of the significance of uptake differences, and generation of high quality figures for data presentation is not yet available. Here we describe the Deuterium Exchange Correction and Analysis (DECA) software package, which provides all these downstream processing options for data from the most popular mass spectrometry platforms. The major functions of the software are demonstrated on sample data. Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large data sets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculations of relative deuterium uptake into regions of the protein after such corrections, rigorous statistical analysis of the significance of uptake differences, and generation of high quality figures for data presentation is not yet available. Here we describe the Deuterium Exchange Correction and Analysis (DECA) software package, which provides all these downstream processing options for data from the most popular mass spectrometry platforms. The major functions of the software are demonstrated on sample data. Hydrogen deuterium exchange mass spectrometry (HDX-MS)1 probes protein structure and dynamics by measuring amide proton exchange. HDX reports on solvent-accessible surface area, protein-protein interfaces, and allosteric changes, and the data can be used to constrain docking or homology modeling (1.Mandell J.G. Falick A.M. Komives E.A. Identification of protein-protein interfaces by decreased amide proton solvent accessibility.Proc. Natl. Acad. Sci. U.S.A. 1998; 95: 14705-14710Crossref PubMed Scopus (188) Google Scholar, 2.Truhlar S.M. Croy C.H. Torpey J.W. Koeppe J.R. Komives E.A. Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry.J. Am. Soc. Mass Spectrom. 2006; 17: 1490-1497Crossref PubMed Scopus (50) Google Scholar, 3.Rey M. Sarpe V. Burns K.M. Buse J. Baker C.A. van Dijk M. Wordeman L. Bonvin A.M. Schriemer D.C. Mass spec studio for integrative structural biology.Structure. 2014; 22: 1538-1548Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar, 4.Ramsey K.M. Narang D. Komives E.A. Prediction of the presence of a seventh ankyrin repeat in IkappaBepsilon from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS).Protein Sci. 2018; 27: 1624-1635Crossref PubMed Scopus (6) Google Scholar). Our group recently showed that HDX-MS experiments in which proteins are incubated in a deuterated solvent for seconds to minutes probe microsecond to millisecond motions in samples (5.Markwick P. Peacock R. Komives E. Accurate prediction of amide exchange in the fast limit reveals thrombin allostery.Biophys. J. 2019; 116: 49-56Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar). Two caveats limit HDX-MS analysis. First, HDX-MS resolution is li