From technical innovation to clinical impact: how Patricia Skowronek is making proteomics methods accessible to more researchers

Patricia Skowronek, a postdoctoral researcher working with Prof. Matthias Mann at the Max Planck Institute of Biochemistry , is actively working to make proteomics methods faster, more precise, and more accessible to researchers across disciplines. Taking an educational approach to her work has paid off, with Patricia having noticed more and more researchers at conferences using the methods she has developed. She’s also driven to translate these technical innovations into clinical applications, ensuring they have a real-world impact.

Bridging technical excellence and clinical impact

"What I really like about proteomics is how you can have a look deep down at the proteins that have such a big impact on us," Patricia explains. "I find this very exciting, to have a look at these actors within the cells. And mass spectrometry is such an exciting technology because you have this real life potential, this real life application.” This practical value fascinated Patricia before she started in Prof. Matthias Mann’s group for her Master thesis and continues to drive her today.

While her background in chemistry naturally drew her toward the technical aspects of mass spectrometry, Patricia's motivation extends beyond pure scientific curiosity.

"What really motivates me is seeing how proteomics can help analyse diseases better, to monitor how patients are improving," she says.

This clinical application shapes her approach to method development, where considerations like high throughput become crucial for analysing large numbers of patient samples.

One of Patricia's most significant contributions to the field so far has been the development of py_diAID, a Python tool that helps researchers optimise their mass spectrometry methods. What began as a personal solution to her own research needs has since been embraced by the broader scientific community.

“Over the years, I went to conferences like ASMS and saw how other researchers picked it up. It filled a need in the community – something that surprised me but was also very rewarding."

Breakthrough moments

Her most memorable scientific breakthrough came during the development of a new, highly sensitive and fast scanning mode called synchro-PASEF. While examining raw data from collaborative work with Bruker, Patricia discovered a phenomenon that gives synchro-PASEF its high selectivity.

"This was such a great moment, to look into the data and suddenly see something which we could use for identification mechanisms," she recalls.

"So many things fell into place. It was super cool to see how much it helps to dig deep and be that persistent."

Patricia refers to the figure below, showing the 'lock and key mechanism' of synchro-PASEF: In this example, one peak is divided into two parts, which must be fitted together again. The correct linking of fragments to their precursors can serve as a criterion for identifying peptides.

With the scan mode now also being integrated into py_diAID, Patricia is keen to see whether it will be picked up by the community as well as dia-PASEF was.

Making proteomics accessible

Beyond technical innovation, Patricia is passionate about making proteomics more accessible to researchers across disciplines. This commitment is evident in her recent Nature Protocols paper, which takes an unconventional approach by including an extensive tutorial section alongside the standard methodology. "Many people have access to timsTOFs nowadays and want to use them properly, but they're like, 'How can I learn to use my instrument to its full potential?'" she explains.

"I find it personally very important to not only conduct top research, which pushes the boundaries of what’s possible, but also to make it accessible so that anyone can use it.”

That’s why the first part discusses how to get the most out of these methods and the instruments, thereby demystifying PASEF method optimisation. This is followed by a step-by-step guide for PASEF workflows. Patricia’s group also made sure to collect and include a list of issues they encountered and their troubleshooting. “It’s very collective. Working on mass specs is a constant challenge, but the problems you encounter as a researcher are often similar, so hopefully this helps others to make sure that performance is top.”

Read the full paper here.

The evolution of standardisation

This push toward standardisation and accessibility reflects a broader evolution in the field. Early in her career, Patricia spent considerable time manually preparing chromatography columns, a process that was both time-consuming and inconsistent. "Column packing was such a tough job. While pushing our own research projects, we couldn't spend all our time on it to make sure that every single column is working perfectly," she recalls. “It was a lot of trial and error. Will the column be good or bad? Do I have to pick a better one? Is there even a better one in the stack?”

Her lab's transition to IonOpticks Aurora Series columns exemplifies this shift toward standardisation.

"I feel like the introduction of IonOpticks columns lowers the barrier of entry, because I’ve adjusted my methods to these setups and gradients. It was more than worth it to have this plug-and-go connection and save time. It's so good to pick any column and it works. I'm super thankful to focus more on actual research than on preparing lab equipment.”

It hasn’t just saved time – it has opened up whole new possibilities. Patricia highlights research that requires high sensitivity such as measuring single cells, where samples amounts are very small. “Deep visual proteomics (DVP) often falls into this category. Making our own columns that are compatible with these gradients, that have super low flow rates and high sensitivity was something we didn’t manage ourselves.”

From lab to life-saving applications

The impact of such standardisation becomes particularly apparent when considering recent breakthroughs in clinical applications. Patricia points her colleague Thierry Nordmann 's study published in 2024 in Nature, where spatial proteomics analysis led to the discovery of a treatment for a lethal skin disease.

“In our group, DVP is developing very rapidly. For different diseases, it lets you look more deeply into the cells and the underlying disease mechanisms. That is something I find super exciting," she says, "to see how the research we do now goes in a direction where it can save people's lives."

Looking to the future

Looking ahead, Patricia remains optimistic about the field's trajectory, particularly as technical innovations continue to enable deeper insights into disease mechanisms. Her work exemplifies how advancing the technical frontiers of proteomics, while maintaining accessibility at the same time can accelerate the path from scientific discovery to clinical impact. "There's just so much coming to the proteomics field—it's moving so fast," she reflects. But through her commitment to both innovation and education, Patricia is helping ensure that this rapidly advancing field remains accessible to researchers at all levels. Ultimately, she is working toward her goal of improving patient outcomes through proteomics research.

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