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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.

Commercial software for analysis of the HDX-MS data

Maintained commercial tools for analysis of HDX-MS data:

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.

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. HDsite; publication.
  4. PyHDX; publication; repository; web server.
  5. Salmas et al., publication; web server.
  6. Saltzberg et al., publication part of IMP
  7. Skinner et al., 2019: publication; repository.

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. Hamuro et al., 2020: Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry.
  3. Masson et al., 2019: Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.
  4. Venable et al., 2012: Subzero Temperature Chromatography for Reduced Back-Exchange and Improved Dynamic Range in Amide Hydrogen/Deuterium Exchange Mass Spectrometry.
  5. Wei et al., 2014: Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications.
  6. Walters et al., 2012: Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.

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

HDX-MS datasets

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