“Proteomics Must Become More Multidimensional”: Experts Discuss the Future of Proteomics

Advances in separation technologies, mass spectrometry, and bioinformatics have shaped modern proteomics. Today, increasingly sophisticated technologies enable proteomic analysis at a scale and speed once unimaginable.

The field of proteomics is now at a turning point, where converging technologies and omics have the potential to reveal new insights into how proteins modify cell function and, in turn, influence human health and disease.

To learn more about what the future of proteomics may look like, Technology Networks asked five leading proteomics experts one question: “Looking ahead to the next decade, what do you see as the most transformative developments on the horizon for proteomics—whether in technology, data analysis, or real‑world clinical impact—and why?”

Gary Patti, PhD, Michael and Tana Powell Professor at Washington University in St. Louis, and CSO of Panome Bio

“Proteomics has already been around for a few decades, but the last handful of years have probably been the most exciting. During that time, we’ve seen an entirely new experimental approach for performing proteomics take off, based on affinity technologies. This has expanded the field to clinicians profiling large cohorts and to scientists for whom proteomics was previously largely inaccessible. Concomitantly, the field of mass spectrometry has also rapidly advanced. The speed, throughput, and sensitivity of the latest instruments have transformed what is possible. So, we really are at a defining moment where suddenly we can do experiments that weren’t imaginable a decade ago.

“Looking ahead, I think what’s most exciting is the scalability.

“Millions and millions of people have had their genomes sequenced. In contrast, very few people have had their proteomes measured, mostly because the technology has not been available. That is no longer a limitation.

“Through CROs such as Panome Bio, it’s now possible to do proteomics at the population scale on huge numbers of people. I truly believe it’s going to change medicine, redefining the way we think about diseases and revealing new treatments.”

Simon Fredriksson, PhD, CEO and co-founder at Pixelgen Technologies

“Tremendous advancements have been made in proteomics. We’ve demonstrated that the underlying chemistry of proteomics can successfully scale to generate consistent, high-quality data across large numbers of cells and experiments. But the field is now at an inflection point.

“The next wave of innovation will come not just from measuring protein abundance but from understanding how proteins interact within cells—their spatial organization and proximity to each other. In other words, proteomics must become more multidimensional, and that will require that we rethink what constitutes meaningful proteomics data.

“I expect an even greater emphasis on single-cell analysis, because bulk measurements often obscure critical biology. We’re going to see significant strides in mapping protein networks, along with transformative innovation in the tools and analytics needed to support this shift, which will ultimately move us closer toward precision drug development and diagnostics, and broader clinical impact.”

Simone Sidoli, PhD, associate professor at the Albert Einstein College of Medicine

“The most transformative shift will be when proteomics can reliably predict phenotypes rather than just describe molecular composition. Right now, protein identity alone explains surprisingly little about biological state. A 10-year-old and a 90-year-old share largely the same proteome at the level of protein lists, yet their phenotypes are profoundly different.

“The field has been very good at measuring ‘what is there’, but much less effective at explaining ‘what it does’ in context.

“Bridging this gap will require moving into higher-order protein biology. The key layers likely include protein folding and conformational states, dynamic protein interactions, and subcellular localization.”

Michael Snyder, PhD, Stanford W. Ascherman Professor of Genetics at Stanford University

“Proteomics is rapidly moving to the forefront thanks to increased throughput, sensitivity, and lower costs. Large-scale proteomics projects are now moving into the mainstream, and these will become integrated into a multiomics understanding of human biology and health. By the end of the decade, I expect it, along with metabolomics, to become routine much like transcriptomics is today. I hope advances in post-translational modifications will also enable large-scale studies to emerge. Finally, spatial single cell proteomics is now emerging and will also become more widespread, providing highly informative insights for a detailed understanding of biology and health.”

Jennifer Geddes-McAlister, PhD, associate professor at the University of Guelph

“Over the next decade, transformations in the diversity and accessibility of proteomics applications will be prominent across scientific disciplines. For example, the application of proteomics (both mass spectrometry-based and non-mass spectrometry-based) will gain in popularity. This will include adaptation for clinical use, such as diagnosing and monitoring disease, as well as identifying and prioritizing biomarkers of disease. We will see these same concepts and workflows applied to other areas, such as environmental monitoring and precision agriculture, to transform exposome research and the interconnectivity with disease, alongside strategies to enhance global food safety and security.

“These transformative developments will be attributed to advances in instrumentation and the versatility of computational tools for robust and reproducible data analysis, as well as a clear integration of expertise and vision across the international proteomics community. Together, this will drive new collaborations (like One Health) and bring together stakeholders to translate biological discoveries into translational applications.”