HDExaminer PRO: High-Confidence HDX-MS Software for Fast Epitope Mapping
Confidently identify the binding site — FAST
HDExaminer™ PRO is an advanced hydrogen deuterium exchange (HDX-MS) software solution within the CHRONECT™ Studio platform, purpose-built for fast, high-confidence HDX data analysis. By automating deuterium uptake analysis, peptide-level HDX mapping, and complex multi-timepoint workflows, it removes manual processing steps that slow you down and introduces objective, reproducible results you can trust for epitope identification and binding-site characterization.
Designed for researchers in pharma, biotech, academia, and contract research organizations, HDExaminer PRO turns intricate hydrogen deuterium exchange protocols into an intuitive, guided workflow, helping you move from HDX spectra to structural insight significantly faster. Formerly known as AutoHX, the software was enhanced and renamed after Trajan acquired it in 2024.
Accelerating discovery at the world’s leading labs
Precision & Compliance Without the Manual Burden
Ensuring the safety of food products is your top priority. Mineral oil hydrocarbons present serious health risks and are tightly regulated. Automated CHRONECT MOSH/MOAH workstations by Trajan enable you to…Trusted by scientists who need speed, accuracy, and confidence
Traditional HDX-MS data analysis can be slow, subjective, and error-prone. HDExaminer PRO changes the game with:
2-5 minutes per data file for 1,000 peptides
Effortlessly handle multi-timepoint, multi-state experiments.
Verify peptides using data-independent acquisition (DIA) data – not just static lists.
10x more data points per peptide vs. conventional HDX software.
Guided workflow makes complex HDX project setup easy.
Heatmaps, volcano plots, peptide maps (exportable to PyMOL, Chimera), and kinetics plots.
Quick assessment of HDX data quality and project results.
Export full result bundles including spreadsheets, images, and publication-ready plots
Purpose-built for your protein characterization needs
Accurate
Unmatched precision with verified peptides and redundant measurements.
Fast
Process large datasets in minutes, not weeks. Accelerating drug discovery, publications, and HDX-MS services.
Smart
Transform raw mass spectrometry data into actionable insights without the need for manual intervention.
“Integrating the CHRONECT MOSH/MOAH workstation into our lab has been a game-changer. We’re able to handle more samples in less time, and the consistency across runs is remarkable. It’s become an essential part of our workflow for detecting mineral oil contaminants with confidence.”
“Integrating the CHRONECT MOSH/MOAH workstation into our lab has been a game-changer. We’re able to handle more samples in less time, and the consistency across runs is remarkable. It’s become an essential part of our workflow for detecting mineral oil contaminants with confidence.”
“Integrating the CHRONECT MOSH/MOAH workstation into our lab has been a game-changer. We’re able to handle more samples in less time, and the consistency across runs is remarkable. It’s become an essential part of our workflow for detecting mineral oil contaminants with confidence.”
Download Center
HDExaminer™ PRO - A paradigm shift in rapid and accurate processing of HDX experiments.
How to Use HDExaminer PRO Software
Whether you’re new to HDExaminer PRO or need a refresher, this step-by-step video tutorial series will get you up and running with confidence.
Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology.
Nat Commun 15, 2200 (2024).
HDX-DIA Concepts & Fundamentals
Lets dive into the science behind hydrogen–deuterium exchange (HDX) paired with mass spectrometry
Examining Instrumental Factors Influencing the Performance of Data-Independent Acquisition Methods in Hydrogen/Deuterium Exchange Mass Spectrometry.
Analytical Chemistry 97, 8011–8020 (2025)
FAQs
CHRONECT Studio is a comprehensive structural biology software platform that hosts a suite of specialized applications, each designed for different purposes. HDExaminer PRO is one of these applications, purpose-built for HDX-MS data analysis.
Yes – we encourage current HDExaminer users to explore HDExaminer PRO. Simply contact us, and our team will provide a demo license along with guidance to help you get started.
HDExaminer PRO is a next-generation HDX-MS analysis solution that introduces significant advancements over the original HDExaminer. While HDExaminer offers semi-automated analysis based on a static peptide list, HDExaminer PRO leverages an additional dimension of data that conventional tools cannot fully exploit. This enables two key capabilities:
- Peptide Identification Validation: HDExaminer PRO incorporates an automated authentication step that directly validates peptide identities during analysis — improving confidence and reducing reliance on external peptide lists.
- Enhanced Accuracy Through Redundancy: The software generates multiple layers of corroborative measurements for each peptide, improving precision, reducing false positives, and delivering higher-confidence results.
These innovations allow HDExaminer PRO to deliver superior speed, accuracy, and reliability – setting a new standard for automated HDX-MS data analysis.
Yes, we offer special pricing for academic institutions. Please contact our team to learn more about available discounts and how to qualify.
Yes, we provide virtual demos to showcase the software’s capabilities, along with demo licenses so you can try HDExaminer PRO firsthand. Contact our team to schedule your demo and receive access.
HDExaminer PRO is offered as an annual subscription license, which includes software updates and standard support throughout the subscription period.
Yes, you may use conventional MS1 HDX data, but without the additional DIA dimension the results will need to be manually curated more often
Discuss pricing and get your FREE demo
HDExaminer PRO is available via annual subscription for both commercial and academic users. Discounts are available for early adopters, multi-seat licenses, and hardware bundles. Ready to see how HDExaminer PRO can accelerate your HDX-MS research? Contact us today to discuss pricing and start your free demo.
Maximize your workstation performance with expert training and ongoing support
Value description i
Value description i
Value description i