DynamX HDX Data Analysis Software 3.0

Significance of the topic

HDX MS is a powerful tool for probing protein structure and interactions. Automating data processing and visualization accelerates insights, improves reproducibility, and supports complex studies in biopharma and academia.

Study objectives and overview

DynamX HDX Data Analysis Software 3.0 aims to streamline HDX MS workflows by automating spectrum selection, mass shift measurement, and comparative analysis across replicates, states, and time courses.

Methodology and Used Instrumentation

The software integrates with UPLC M-Class Systems and Waters MS platforms (SYNAPT, Xevo) and MassLynx, leveraging sharper chromatographic peaks and MS E detection. Key capabilities include:

• Automated processing of intact protein, peptide digest, and ETD fragmentation data.
• Support for ion mobility (HD MS E) to enhance protein coverage.
• Localization of residue-level structural changes via ETD fragment analysis.
• Export of HDX data to PyMOL for structural modeling.

Main results and discussion

DynamX 3.0 demonstrably reduces HDX data analysis time by automating complex tasks. Comparative visualizations such as uptake curves, butterfly difference plots, and coverage maps enable rapid identification of local conformational changes and binding sites. ETD-based analysis achieved amino acid resolution for protein–ligand interactions, as illustrated by z-ion uptake differences in EGFR–Adnectin complexes.

Benefits and practical applications

The platform supports diverse HDX MS studies including:

• Comparability testing for native vs. mutant or biosimilar proteins.
• Drug candidate binding and ligand screening at multiple time points.
• Protein–protein interaction mapping in complex assemblies.
• Quality control and batch-to-batch comparability in biopharma.

Future trends and applications

Emerging directions include cloud-based and AI-assisted HDX data processing, real-time feedback during experiments, deeper coverage for membrane and large complex proteins, and integration with multi-omics platforms to correlate conformational dynamics with functional outcomes.

Conclusion

DynamX HDX Data Analysis Software 3.0 offers a robust, user-friendly solution for high-throughput HDX MS interpretation, fostering faster, more reliable insights into protein structure and interactions.

References

1. Ramamurthy et al., Structure, 2012, 20, 259–269.
2. Waters Corporation. DynamX HDX Data Analysis Software 3.0 Whitepaper, 2015.