HDExaminer 3.42 is a minor update in the 3.x series of HDExaminer, a specialized software package for Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) data analysis. Developed originally by Sierra Analytics and now a product of Trajan Scientific and Medical (since February 2023), it streamlines the processing, visualization, and interpretation of HDX-MS experiments. These experiments are crucial for studying protein structure, dynamics, and interactions in fields like pharmaceuticals, biochemistry, and structural biology.

HDExaminer excels at handling data from various mass spectrometers (e.g., Thermo, Waters, Bruker), providing reproducible deuteration uptake calculations, confidence scoring, and export options for further analysis (e.g., PyMOL scripts for 3D visualization). Version 3.42, released around mid-2025 as a point release, focuses on bug fixes, performance tweaks, and minor UI refinements rather than major feature additions. It maintains backward compatibility with projects from earlier 3.x versions but requires the latest Trajan licensing for full access.

Key highlights:

  • Release Timeline: Part of the ongoing 3.x branch; 3.4 was highlighted in early 2024, with incremental updates like 3.42 addressing user feedback on stability for large datasets.
  • System Requirements: Windows 10/11 (64-bit); compatible with Thermo Xcalibur, Waters MassLynx, and Bruker DataAnalysis formats. Minimum 8 GB RAM recommended for datasets >1 GB; no specific GPU needs.
  • Licensing: Subscription-based through Trajan; includes integration with CHRONECT™ HDX automation platforms for seamless workflow from sample prep to analysis.

New Features and Improvements in HDExaminer 3.42

As a point release, 3.42 builds on 3.4’s foundation (e.g., Bruker timsTOF support and MS “stick” data handling) with targeted enhancements:

  • Stability Fixes: Resolved crashes in peptide list imports for datasets exceeding 500 peptides, improving reliability for high-throughput pharma screening.
  • Visualization Tweaks: Enhanced heat map rendering speed (up to 20% faster) and added optional export to interactive HTML plots for easier sharing.
  • Statistics Refinements: Minor updates to confidence rating algorithms, incorporating user-defined thresholds for low-signal regions.
  • Integration Updates: Better compatibility with HDXBoxeR R package for downstream statistical analysis of multi-state protein datasets.