The Background
Advancing complex structural biology at The Broad Institute
The Broad Institute of MIT and Harvard is an independent, nonprofit biomedical research organization based in Cambridge, Massachusetts. It brings together scientists across disciplines and partner institutions to tackle ambitious challenges in biology and disease, with a mission centered on turning biological insight into impact for patients.
For this customer story, we interviewed Malvina Papanastasiou, Ph.D (Senior Group Leader and Research Scientist), and Shaunak Raval, Ph.D (Postdoctoral Associate), researchers at The Broad Institute who apply HDX-MS to support diverse structural biology research and collaborative projects. Their work spans internal Broad Institute teams, the broader academic community, and partners in pharmaceutical and biotechnology sectors.
HDX-MS for increasingly diverse research questions
The scientific questions addressed by the team are equally diverse, including identification of ligand-binding sites, epitope mapping, and characterization of conformational changes in AI-designed proteins, membrane proteins, and large protein complexes.
For some collaborators, HDX-MS provides an early structural view before committing resources to techniques such as X-ray crystallography or cryo-electron microscopy. For others, it provides a way to investigate specific interactions or to support larger therapeutic development programs.
As the team's projects expanded in scope and the range of HDX-MS applications grew, efficient analysis of large and complex datasets became essential to supporting ongoing research.
The Challenge
High-quality experiments still created a significant analysis burden
Before adopting HDExaminer PRO, the Broad Institute team had already invested considerable effort in optimizing its HDX-MS methods for reproducibility and efficiency. The consistent data produced by the CHRONECT HDX-MS workflow allowed the team to establish fixed peptide boundaries and minimize manual quality control steps.
However, data analysis remained time-intensive, particularly as the number of proteins, ligands, comparisons, and experimental variables increased. Conventional MS1-based analysis limited throughput, creating a bottleneck for larger comparative studies.
The opportunity wasn't simply to analyze the same data faster. It was to make larger, more complex HDX-MS studies practical.
The Solution
Bringing DIA and streamlined analysis together with HDExaminer PRO
HDExaminer PRO introduced a more scalable approach to HDX-MS data analysis, combining DIA workflows, fragment-supported analysis, statistical tools, and a streamlined processing environment.
For the Broad Institute team, fragment-level evidence is particularly valuable when peptide assignments are ambiguous. In proteins such as histones, where sequences can be highly similar, fragment information can help distinguish related peptides and rule out incorrect possibilities. That, in turn, reduces the amount of manual review that previously consumed valuable researcher time.
HDExaminer PRO does not remove the need for HDX-MS expertise. Researchers still need to design experiments appropriately, understand acquisition and DIA methods, evaluate results, and intervene when necessary. Instead, the combination of CHRONECT HDX-MS and HDExaminer PRO helps practitioners spend less time on avoidable manual analysis—and more time interpreting results and advancing the science.
"The barrier to entry has been lowered”
— Shaunak Raval, Ph.D., The Broad Institute
The Outcome
More speed. More capacity. More ambitious HDX-MS.
The biggest change for the Broad Institute team is not simply faster data processing. It is the scale of the projects they can now consider.
Larger and more complex studies can be performed and analyzed in significantly shorter timeframes, allowing the team to take on work that would previously have required substantially more time and resources.
The team described a 96-well binder-screening project requiring high-throughput mapping and an answer within a week as something they can now say yes to—an expectation that previously would not have been practical because data analysis was a bottleneck.
Shifting the bottleneck
The increase in processing capacity has been significant enough that the constraint can shift away from data analysis itself. In some cases, available mass-spectrometer capacity may become more limiting than the amount of HDX-MS data the team can process.
That creates new possibilities for applications such as biologics research, where the Broad Institute is exploring higher-throughput approaches to binder screening and bringing epitope-paratope mapping earlier into therapeutic development. Learn how it was done, PMCID: PMC12950381.
A different way to think about HDX-MS
HDX-MS has traditionally carried a reputation for being slow and complex. The Broad Institute's experience with DIA methods and HDExaminer PRO points toward a different model, one in which HDX-MS can be sensitive, robust, and high throughput.
That shift opens the door to using HDX-MS not only to answer individual structural questions, but increasingly as part of larger screening workflows.
“If there is one thing that you take…it's sensitive, it's robust, and it's high throughput.”
— Malvina Papanastasiou, Ph.D., The Broad Institute
The Takeaway
When analysis can keep pace, the science can scale
For laboratories with growing HDX-MS project volume, the value of a more efficient analysis workflow extends beyond time savings. Reducing the burden of manual processing can create capacity for larger studies, more comparisons, and new high-throughput applications—while keeping scientific expertise at the center of the workflow.
