Manually curated lists of software, publications and other resources related to the analysis of HDX-MS data.
Open, free and maintained tools for analysis of HDX-MS data:
- DECA: publication; repository.
- deMix: publication; access on request.
- Deuteros 2.0: publication; repository. Version 1.0: publication; repository.
- ExMS2: publication; MATLAB package. EXMS: publication; MATLAB package.
- HaDeX: publication; repository, web server.
- HDXanalyzer publication; RPY package.
- HDX-Viewer: publication; web-server; repository.
- Hexicon 2: publication; access on request.
- HD-eXplosion: publication; web-server; repository.
- HX-Express v2: publication; availability.
- MEMHDX: publication; web server.
- QUDeX-MS publication; stand-alone tool.
- The Deuterium Calculator publication; repository.
Maintained commercial tools for analysis of HDX-MS data:
- BioPharma Findfer (MassAnalyzer) link
Non-maintained (no updates for at least five years) tools for analysis of HDX-MS data:
Scripts and data for HDX-MS data analysis:
- HDX Simulations: Kan ZY, Robert Bradshaw.
- HDXrate: repository.
- H/D exchange rate excel spreadsheets: Englander group website.
- HDXer: repository.
Publications and software for HR HDX-MS analysis:
- Babic et al., 2019: publication. Follow-up to HDSite.
- Gessner et al., 2017: publication.
- Kan et al., 2013, (HDsite): publication.
- Smit et al., 2021, (PyHDX): publication; repository; web server.
- Salmas et al., 2021, (HDXmodeller): publication; web server.
- Saltzberg et al., 2017: publication; part of IMP
- Skinner et al., 2019: publication; Stofella et al., 2022: publication; repository.
- Seetaloo et al, 2022, (HDfleX): publication; download
HDX-MS data analysis methodology, focusing on HDX-MS data processing’s computational aspects:
- Althaus et al., 2010: Computing H/D-Exchange rates of single residues from data of proteolytic fragments.
- Bai et al., 1993: Primary structure effects on peptide group hydrogen exchange.
- Best et al., 2006: Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2.
- Bradshaw et al., 2020: Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.
- Claesen et al., 2016: Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.
- Claesen et al., 2019: POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens.
- Dovischenko et al., 2008: Prediction of Residue Status to Be Protected or Not Protected From Hy-drogen Exchange Using Amino Acid Sequence Only.
- Englander et al., 1997: Hydrogen exchange: the modern legacy of Linderstrøm-Lang..
- Fajer et al, 2012: Improved Sequence Resolution by Global Analysis of Overlapped Peptides in Hydrogen/Deuterium Exchange Mass Spectrometry.
- Hageman et al, 2018: Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach.
- Harris et al, 2019: Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS)
- Konermann et al., 2011: Hydrogen exchange mass spectrometry for studying protein structure and dynamics.
- Mazur et al., 2017: The Area Between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies.
- Nguyen et al., 2018: Reference Parameters for Protein Hydrogen Exchange Rates.
- Skinner et al., 2012: Protein hydrogen exchange: testing current models.
- Skinner et al., 2012: Protein dynamics viewed by hydrogen exchange.
- Tajoddin et al. 2020: Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments.
- Zhang et al., 1993: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation..
- Zhang et al., 2012: Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.
- Zhang et al., 2020: Complete Extraction of Protein Dynamics Information in Hydrogen/Deuterium Exchange Mass Spectrometry Data.
The methodology of HDX-MS and advances in HDX-MS experiments design:
- Brown et al., 2017: Bottom-up hydrogen deuterium exchange mass spectrometry: data analysis and interpretation.
- Engen et al., 2022: Simple and Fast Maximally Deuterated Control (maxD) Preparation for Hydrogen–Deuterium Exchange Mass Spectrometry Experiments.
- Hamuro et al., 2020: Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry.
- Lauer et al., 2021: Profiling Structural Alterations During Rab5 Nucleotide Exchange by HDX-MS.
- Masson et al., 2019: Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.
- Venable et al., 2012: Subzero Temperature Chromatography for Reduced Back-Exchange and Improved Dynamic Range in Amide Hydrogen/Deuterium Exchange Mass Spectrometry.
- Wei et al., 2014: Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications.
- Walters et al., 2012: Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.
- Wu et al., 2021: Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein.
Publications and pre-prints showcasing the applications of HDX-MS, where HDX-MS experiments play a crucial role:
- Banos-Mateos et al., 2017: High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.
- Filandrova et al., 2021: Studying Protein–DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.
- Hamdi et al., 2017: Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins.
- Lim et al., 2017: Epitope and Paratope Mapping Reveals Temperature-Dependent Alterations in the Dengue-Antibody Interface.
- Lesne et al., 2020: Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks.
- Masson et al., 2017: Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry .
- Merkle et al., 2018: Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.
- Shukla et al., 2014: Visualization of arrestin recruitment by a G-protein-coupled receptor.
General reviews of HDX-MS experiments, not focusing on a single application, experimental problem, or computational method:
- James et al., 2021: Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.
- Engen et al., 2021: Developments in Hydrogen/Deuterium Exchange Mass Spectrometry.
- Georgescauld et al., 2019: Hydrogen deuterium exchange mass spectrometry applied to chaperones and chaperone-assisted protein folding.
- Mitra et al., 2020: Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins.
- Narang et al., 2020: HDX-MS: An Analytical Tool to Capture Protein Motion in Action.
- Giladi et al., 2020: Hydrogen-Deuterium Exchange Mass-Spectrometry of Secondary Active Transporters: From Structural Dynamics to Molecular Mechanisms.
- Konermann et al., 2011: Hydrogen exchange mass spectrometry for studying protein structure and dynamics.
- Hoofnagle et al., 2003: Protein Analysis by Hydrogen Exchange Mass Spectrometry.
- Englander et al., 1997: Hydrogen exchange: the modern legacy of Linderstrøm-Lang.
- Englander et al., 1996: Mechanisms and uses of hydrogen exchange.
- SAP, Enolase, Barnase, Alpha_lac Salmas et al, link
- SecB Smit et al, link
- SNase Gessner et al, link
- Human 20S proteasomes Lesne et al, link
- Fab fragment of NISTmAb Hudgens et al (1) Hudgens et al (2), link
- XylE, LacY, GlpT Martens et al, link
- HalM2 Habibi et al, link
- Human Hb, Human IgG4 Tsiatsiani et al, link
- SecYEG, SecA Ahdash et al, link
- VDR, RORγ Saltzberg et al, link
- 15-LOX Droege et al link
- human Rag GTPase Anandapadamanaban et al link
- Eukaryotic Ribosome GCN2 Inglis AJ et al link