Over the last decade, mass spectrometry–based proteomics has been on a clear mission: go deeper and go faster. As a field, we have worked hard to close the gap with genomics and transcriptomics, pushing technology to quantify more proteins, in more samples, in less time, at a price point that does not hinder research.
At Biognosys, now part of the Biognosys Group, we have been deeply involved in this journey. From the early days, we believed that every additional protein we could measure increased the chances of finding something important: a biomarker, a pathway, a new drug target that might ultimately make a difference for patients. That belief drove much of our work in discovery proteomics, DIA workflows, and scalable CRO services for biopharma.
But over time, I have come to realize that in chasing numbers, we sometimes lose sight of why we are doing this in the first place.
The Power of One Protein
Back in 2012, Nature named targeted proteomics “Method of the Year.” Interestingly, this was also the area we focused on when we founded Biognosys in 2008. Our early work was centered on building better algorithms and workflows for targeted mass spectrometry because even then, we believed that precision and reproducibility would ultimately matter most.
Our R&D later expanded strongly into DIA, where we became pioneers in software, workflows, and proteomics services that enable deep, cost-effective profiling at scale. DIA has been transformative for discovery science, and it continues to fuel new hypotheses and therapeutic ideas.
Yet, time and again, our customers pull us back to targeted proteomics – especially when the stakes are high.
Because when a clinical team needs to decide whether a drug is working, how to dose a patient, or how to design the next phase of a trial, “relative trends” are no longer enough. What they need are robust, absolute, and reproducible measurements they can trust.
When Proteomics Shapes Clinical Decisions
One example that stands out for me is our collaboration with Kymera Therapeutics. Together, we developed targeted proteomic assays to directly monitor the degradation of specific proteins induced by their drug candidates. These measurements were not academic exercises, they informed critical decisions in clinical trial design and patient dosing for autoimmune diseases, with real consequences for patients and programs alike.
(Nature Medicine, 2023)
Another example is our more recent partnership with the Michael J. Fox Foundation. Here, we are helping to develop highly sensitive targeted assays as part of a global effort to accelerate therapies and biomarkers for LRRK2, the most common genetic risk factor for late-onset Parkinson’s disease. In this setting, assay robustness, sensitivity, and standardization are everything. In this case the SISCAPA technology provides the key to meet these requirements that enables comparisons across cohorts and sites.
Why Targeted Proteomics in a Regulated Environment Matters
Mass spectrometry has made extraordinary progress. Today, we can quantify thousands of proteins in plasma and approach complete proteome coverage in cell lines and tissues at a cost that was unimaginable just a few years ago. This is opening new doors in discovery and target identification across biopharma.
But when it comes to making a real difference in health and disease, the most impact still comes from regulated, targeted assays: single-protein or focused panels, measured with the highest sensitivity and specificity, delivered with absolute quantification and full confidence in the data.
This is exactly why we built our TrueSignature services, delivered under GCP-compliant validation within the Biognosys Group. They reflect years of experience working at the interface of technology, biology, and clinical reality, where data must stand up not only to scientific scrutiny, but also to regulatory requirements and in the future clinical decision-making.
From Proteome Depth to Patient Impact
I remain incredibly proud of how far the field has come in terms of depth and scale. But I am even more proud of the moments when precise protein measurements help answer the questions that truly count: questions about efficacy, safety, and ultimately, patient benefit.
