Making proteoforms mainstream with the Consortium for Top-Down Proteomics
Tyler Ford
September 11, 2025
As the functional variants of proteins, it may seem obvious that studying proteoforms is critical to understanding biology. Yet proteoform-centric studies are not a mainstay of life sciences research. This should be a point of great concern for anyone who hopes to identify the next generation of biomarkers and drug targets. Protein measurements can point us in the right direction in terms of identifying pathways underlying phenotypes, but it is specific proteoforms that contort these pathways into different functional states, including those causing disease. Thus, it is through targeting and altering proteoforms that researchers will create effective next-generation precision medicines and diagnostics.
Like our team at Nautilus, an energetic group of researchers in the top-down proteomics community is not happy with the status quo. They have pioneered the use of top-down mass spectrometry (TDMS) to discover new proteoforms and their relationships to functional biology. They have provided many proof points for the importance of proteoforms across diverse research areas including:
In August we had the privilege of attending the Consortium for Top-Down Proteomics (CTDP) conference where we met with leaders in the top-down community to confront problems with the perception and adoption of proteoform-centric research. Some of our takeaways from the conference can be found below. We look forward to working with members of this community to revolutionize biology by making proteoforms mainstream.
A need for complementary technologies
TDMS workflows are complex. In them, researchers measure mass to charge ratios (m/z) of intact protein molecules, isolate intact proteins with specific m/z values, fragment them, measure the fragments’ m/z values to determine their compositions, and then infer the compositions of the intact proteins from the combination of their fragments. It’s a great technique for identifying and often fully characterizing proteoforms, but as you might imagine, it can get very complicated. Often, extensive protein separation techniques are required to make top-down mass spectra decipherable. Even then, larger proteoforms may produce overly complex signals, and proteoforms with similar m/z values may still be hard to distinguish from one another. Thus, while great for researchers who can optimize protocols to discover new proteoforms, TDMS is not easy to scale for robust and high throughput proteoform quantification. Nonetheless, many researchers deeply associate proteoforms with this complex technique.
Given the complexity of TDMS, the technical prowess of CTDP attendees is incredibly impressive. Until now they’ve had no other technologies for proteoform analyses, but they are open to new technologies and are excited about the future. Presented with up-and-coming technologies like our own Iterative Mapping of proteoforms, researchers in this community see that it’s important to disentangle proteoforms from TDMS. They know TDMS will play a prominent role in proteoform discovery for many years but recognize the need for complementary technologies that can scale to make proteoform studies more approachable and impactful.
A proteoform marketing problem?
Beyond their association with TDMS, proteoforms have an additional problem – many researchers don’t understand what proteoforms are. To study proteoforms one must identify how post-translational modifications (PTMs), isoforms, genetic variation, and more combine in intact proteins. Exploring how these features come together to change the structures and behaviors of full-length proteins is what differentiates proteoform studies and makes them valuable. Yet, many people investigate isolated post-translational modifications or peptides and claim they’re studying proteoforms. This is not possible.
As our own Andreas Huhmer mentioned on a panel at the conference, this has led to a “marketing problem” for the field. Simply put, it’s not possible to get across the great importance of proteoforms when:
- People are discouraged by the complexity of the core technology used to study them.
- Few fully understand what proteoforms are in the first place.
The development of a “Proteoform Alliance”?
To overcome this “marketing problem” some at the conference suggested an important first step of changing the name from the “Consortium for Top Down Proteomcs” to the “Proteoform Alliance” and inviting researchers working with other technologies into the fold. Along the way, they hope the Alliance will focus less on tech specs and more on the impact proteoform studies have on biological understanding. These studies will be bolstered by Alliance-developed proteoform standards that benchmark different technologies and make their measurements comparable.
Driving toward clinical breakthroughs powered by Iterative Mapping of proteoforms
Rebranding to the Proteoform Alliance and focusing on biological breakthroughs backed by standards are great first steps toward making proteoforms mainstream. For our part, we’re actively pursuing partnerships where we hope Iterative Mapping of proteoforms identifies new biomarkers and drug targets. While top-down proteomics has opened our minds to the power of proteoforms, we ultimately aim for the Nautilus Platform to drive clinical applications of proteoform research. We hope stories of clinical breakthroughs powered by proteoforms inundate the biological sciences over the next few years. With the first drafts of these stories already in place thanks to the efforts of the TDMS community, we’re confident we’ll soon make proteoforms mainstream.
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