We are pleased to announce that the HDX-MS robotics platform is now fully operational. After thorough cleaning, replenishing all consumables (ordering the robot needles alone took 7 months…), and completing full calibration and optimization, we now have fully automated HDX-MS sample preparation — from D₂O labeling through quenching to digestion and LC-MS analysis.

We modified a number of steps from the original instrument method for robotic control, and we have achieved significantly improved data reproducibility compared to the original Waters method supplied with the robot.

Another major upgrade we introduced is a new acquisition method (so-called HDX-DIA), which enables automated validation of all HDX-MS data — currently one of the main bottlenecks in the field.

By combining cyclic ion mobility, MSe DIA data acquisition, and state-of-the-art HDX-MS software, we now collect and analyze high-quality data in two dimensions: both MS1 (intact peptide masses) and MS2 (peptide fragmentation and MS analysis of resulting fragments). This enables automated validation of both peptide identity and deuteration levels. As a result, data analysis time has been reduced from typically days to weeks of manual work to just a few hours of computational processing. Our HDX-MS throughput has therefore increased approximately threefold.

We are currently preparing a methodological publication on our new ion mobility and MSe-based approach, and in two weeks we will present it at the HDX-MS 2026 conference in Strasbourg.

František Filandr
Tereza Nešporová