Proteins are the tiny molecular machines that make life work, serving many purposes from building cellular structures to transmitting signals and facilitating chemical reactions in the cell. To perform their functions, proteins often need to interact with one another, and studying these interactions is key to understanding how living systems function. However, proteins are small, complex, and constantly moving, making it difficult to study how they connect to each other.
One of the most powerful ways scientists can study these interactions is through mass spectrometry, a technique that identifies molecules by measuring their weight and electrical charge. A more specialized form, called cross-linking mass spectrometry (XL-MS), uses special chemical “glues” — known as crosslinkers— to bind together proteins that are physically close to each other inside the cell. The bound proteins can then be extracted from the cell and broken down into small fragments called peptides to be read by the mass spectrometer. This helps researchers map not only which proteins interact, but also which parts of the different proteins touch — like freezing a handshake in time.
However, XL-MS has long been limited by its sensitivity. Many important protein interactions are too rare or too weak to detect because their signals are easily drowned out by more abundant peptides.
Now, researchers from the Proteomics Technology Hub at the Vienna BioCenter have shown how a new instrument, the Orbitrap Astral mass spectrometer developed by Thermo Fisher Scientific, can overcome these limitations. In a study led by Fränze Müller and Karl Mechtler, the team compared the Astral to an earlier-generation instrument and found it could identify over 40% more protein crosslinks, even from very low sample amounts.
The team also fine-tuned the experimental setup to improve how crosslinked peptides — the linked pieces of proteins — are separated and detected during XL-MS. By adjusting several technical steps in the analysis process — such as ion filtering, collision energy, and separation time — they could further boost performance. Using the same sample, the team was able to detect and explore protein connections that were previously invisible, including surface-level protein interactions, but also rare connections buried deep inside the proteins themselves.
“This technology lets us detect weaker, harder-to-find interactions,” says Fränze Müller, the study’s first author. “It’s like turning up the brightness on a very dim picture — suddenly you can see details you didn’t know were there.”
“Using this improved protocol, scientists can better validate structural models, identify protein assemblies, and detect transient interactions in complex samples,” explains Karl Mechtler. “This resource has enormous technological significance for researchers at the Vienna Bio-Center Campus, who benefit from the advancements developed at the Proteomics Tech Hub.”
The study, published in Nature Communications, highlights the Vienna BioCenter’s Proteomics Technology Hub as a center for innovation in high-precision protein research, offering powerful tools and expertise for scientists around the world.
Original Publication
Müller, F., Birklbauer, M.J., Bubis, J. et al. Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral. Nat Commun16, 9877 (2025). https://doi.org/10.1038/s41467-025-64844-7
About the Vienna BioCenter Proteomics Tech Hub
The Proteomics Tech Hub, headed by Karl Mechtler and shared between three institutes at the Vienna BioCenter (IMBA, IMP and GMI), aims to advance cutting-edge proteomics methods with a strong focus on single-cell proteomics. The team establishes and designs novel protocols to improve the sensitivity of protein identification, protein quantification, and cross-linking technology.