Manually curated lists of software, publications and other resources related to the analysis of HDX-MS data.

Open software for analysis of the HDX-MS data

Open, free and maintained tools for analysis of HDX-MS data:

1. DECA: publication; repository.
2. deMix: publication; access on request.
3. Deuteros 2.0: publication; repository. Version 1.0: publication; repository.
4. ExMS2: publication; MATLAB package. EXMS: publication; MATLAB package.
5. HaDeX: publication; repository, web server.
6. HDXanalyzer publication; RPY package.
7. HDX-Viewer: publication; web-server; repository.
8. Hexicon 2: publication; access on request.
9. HD-eXplosion: publication; web-server; repository.
10. HX-Express v2: publication; availability.
11. MEMHDX: publication; web server.
12. QUDeX-MS publication; stand-alone tool.
13. The Deuterium Calculator publication; repository.

Commercial software for analysis of the HDX-MS data

Maintained commercial tools for analysis of HDX-MS data:

1. BioPharma Findfer (MassAnalyzer) link

Deprecated tools for analysis of the HDX-MS data

Non-maintained (no updates for at least five years) tools for analysis of HDX-MS data:

Repositories

Scripts and data for HDX-MS data analysis:

1. HDX Simulations: Kan ZY, Robert Bradshaw.
2. HDXrate: repository.
3. H/D exchange rate excel spreadsheets: Englander group website.
4. HDXer: repository.

High-resolution HDX-MS

Publications and software for HR HDX-MS analysis:

1. Babic et al., 2019: publication. Follow-up to HDSite.
2. Gessner et al., 2017: publication.
3. Kan et al., 2013, (HDsite): publication.
4. Smit et al., 2021, (PyHDX): publication; repository; web server.
5. Salmas et al., 2021, (HDXmodeller): publication; web server.
6. Saltzberg et al., 2017: publication; part of IMP
7. Skinner et al., 2019: publication; Stofella et al., 2022: publication; repository.
8. Seetaloo et al, 2022, (HDfleX): publication; download

Analysis of HDX-MS data

HDX-MS data analysis methodology, focusing on HDX-MS data processing’s computational aspects:

1. Althaus et al., 2010: Computing H/D-Exchange rates of single residues from data of proteolytic fragments.
2. Bai et al., 1993: Primary structure effects on peptide group hydrogen exchange.
3. Best et al., 2006: Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2.
4. Bradshaw et al., 2020: Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.
5. Claesen et al., 2016: Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.
6. Claesen et al., 2019: POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens.
7. Dovischenko et al., 2008: Prediction of Residue Status to Be Protected or Not Protected From Hy-drogen Exchange Using Amino Acid Sequence Only.
8. Englander et al., 1997: Hydrogen exchange: the modern legacy of Linderstrøm-Lang..
9. Fajer et al, 2012: Improved Sequence Resolution by Global Analysis of Overlapped Peptides in Hydrogen/Deuterium Exchange Mass Spectrometry.
10. Hageman et al, 2018: Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach.
11. Harris et al, 2019: Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS)
12. Konermann et al., 2011: Hydrogen exchange mass spectrometry for studying protein structure and dynamics.
13. Mazur et al., 2017: The Area Between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies.
14. Nguyen et al., 2018: Reference Parameters for Protein Hydrogen Exchange Rates.
15. Skinner et al., 2012: Protein hydrogen exchange: testing current models.
16. Skinner et al., 2012: Protein dynamics viewed by hydrogen exchange.
17. Tajoddin et al. 2020: Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments.
18. Zhang et al., 1993: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation..
19. Zhang et al., 2012: Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.
20. Zhang et al., 2020: Complete Extraction of Protein Dynamics Information in Hydrogen/Deuterium Exchange Mass Spectrometry Data.

Design of HDX-MS experiments

The methodology of HDX-MS and advances in HDX-MS experiments design:

1. Brown et al., 2017: Bottom-up hydrogen deuterium exchange mass spectrometry: data analysis and interpretation.
2. Engen et al., 2022: Simple and Fast Maximally Deuterated Control (maxD) Preparation for Hydrogen–Deuterium Exchange Mass Spectrometry Experiments.
3. Hamuro et al., 2020: Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry.
4. Lauer et al., 2021: Profiling Structural Alterations During Rab5 Nucleotide Exchange by HDX-MS.
5. Masson et al., 2019: Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.
6. Venable et al., 2012: Subzero Temperature Chromatography for Reduced Back-Exchange and Improved Dynamic Range in Amide Hydrogen/Deuterium Exchange Mass Spectrometry.
7. Wei et al., 2014: Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications.
8. Walters et al., 2012: Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.
9. Wu et al., 2021: Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein.

Applications of HDX-MS

Publications and pre-prints showcasing the applications of HDX-MS, where HDX-MS experiments play a crucial role:

1. Banos-Mateos et al., 2017: High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.
2. Filandrova et al., 2021: Studying Protein–DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.
3. Hamdi et al., 2017: Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins.
4. Lim et al., 2017: Epitope and Paratope Mapping Reveals Temperature-Dependent Alterations in the Dengue-Antibody Interface.
5. Lesne et al., 2020: Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks.
6. Masson et al., 2017: Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry .
7. Merkle et al., 2018: Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.
8. Shukla et al., 2014: Visualization of arrestin recruitment by a G-protein-coupled receptor.

General reviews

General reviews of HDX-MS experiments, not focusing on a single application, experimental problem, or computational method:

1. James et al., 2021: Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.
2. Engen et al., 2021: Developments in Hydrogen/Deuterium Exchange Mass Spectrometry.
3. Georgescauld et al., 2019: Hydrogen deuterium exchange mass spectrometry applied to chaperones and chaperone-assisted protein folding.
4. Mitra et al., 2020: Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins.
5. Narang et al., 2020: HDX-MS: An Analytical Tool to Capture Protein Motion in Action.
6. Giladi et al., 2020: Hydrogen-Deuterium Exchange Mass-Spectrometry of Secondary Active Transporters: From Structural Dynamics to Molecular Mechanisms.
7. Konermann et al., 2011: Hydrogen exchange mass spectrometry for studying protein structure and dynamics.
8. Hoofnagle et al., 2003: Protein Analysis by Hydrogen Exchange Mass Spectrometry.
9. Englander et al., 1997: Hydrogen exchange: the modern legacy of Linderstrøm-Lang.
10. Englander et al., 1996: Mechanisms and uses of hydrogen exchange.

HDX-MS datasets

• 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