HD desktop: an integrated platform for the analysis and visualization of H/D exchange data

Area of Science:

• Biochemistry
• Analytical Chemistry
• Computational Biology

Background:

• Hydrogen/deuterium exchange (HDX) mass spectrometry is a powerful technique for studying protein dynamics and interactions.
• Analyzing HDX data can be complex and time-consuming, requiring specialized software tools.
• Existing workflows often lack integration, hindering efficient data processing and visualization.

Purpose of the Study:

• To introduce HD Desktop, an integrated software platform designed to enhance the analysis of HDX mass spectrometry data.
• To provide a user-friendly, web-based application for streamlined HDX data management and visualization.
• To offer a robust solution for the broader HDX research community.

Main Methods:

• Development of a web-based application integrating data extraction and visualization tools.
• Implementation of a relational database for enhanced performance, data storage, and retrieval.
• Automated peptide data consolidation for 2D data rendering using established and novel approaches.
• Inclusion of retention time determination via theoretical isotope fitting.

Main Results:

• HD Desktop provides a unified interface for navigating HDX data from peptide to experiment levels.
• The software enables real-time updates of aggregate graphs as data manipulations occur.
• Integrated database ensures efficient data handling and robust storage.
• Automated data consolidation and retention time determination streamline the analysis workflow.

Conclusions:

• HD Desktop offers an efficient and manageable workflow for HDX mass spectrometry data analysis.
• The platform addresses the needs of the HDX community by integrating key functionalities.
• HD Desktop is freely available as a web tool, promoting wider adoption and research advancement.