Nautilus at US HUPO 2025 – Bringing the proteome into focus with the Nautilus Proteome Analysis Platform

At US HUPO 2025 in Philadelphia, we shared novel data generated by the Nautilus^TM Proteome Analysis Platform and focused on how that data can be applied to revolutionize our understanding of biology and disease. In this blog post, we share some of our key takeaways from the event and encourage you to reach out or access our content from the conference to learn more.

Tau proteoforms provide an in-depth look at Alzheimer’s models and the human brain 

At our lunch seminar, we had the honor of hosting Tara Tracy, Ph.D. from the Buck Institute for Research on Aging. She started the session with a great overview of the many roles the microtubule associated protein tau plays in neurodegenerative diseases such as Alzheimer’s disease (AD). She also introduced the audience to the idea that tau comes in many molecular variants, proteoforms, and that groups of tau proteoforms have been associated with the pathologies of neurodegenerative diseases. While it’s known that tau is heavily modified in these diseases, it is neither clear which specific tau proteoforms are important, nor is it clear how these proteoforms arise and interact. This limits our understanding of AD and the potential for biomarker discovery and therapeutic development.

By developing a platform that can rapidly measure single-molecule proteoforms, we hope to enable researchers to resolve the links between proteoforms and biological function. Toward this end, we shared data demonstrating how our platform can measure thousands of tau proteoforms with abundances varying over 3 orders of magnitude in:

• Neuronal organoids 
• Multicellular integrated brains (MiBrains) 
• Mouse brains
• And for the first time, human brains

Covering this range of model systems, and for the first time the human brain, shows our method effectively measures proteoforms in key biomedical samples. Seeing this, members of the audience had deep questions like: 

• How adaptable is the technology to other proteins?
  Highly adaptable – we’ve begun work with other proteins and are limited only by what probes are available to measure specific modifications. We extensively validate commercial probes for these assays to ensure we’re providing accurate, single-molecule views of the proteoform landscape.
• What determines the types of proteoforms we can measure?
  Here too, we are limited only by the probes that are available. 
• What determines our dynamic range?
  With flow cells that accommodate up to 10-billion protein molecules, we’ve designed our platform to quantify proteins varying in abundance over 10 orders of magnitude. Unlike broadscale proteomic analyses which use multi-affinity reagents (discussed below), targeted proteoform analyses use commercial antibodies that detect specific modifications. Thus, the dynamic range of a targeted proteoform assay is limited by the commercial probes that are available, and 3 orders of magnitude is far from the upper limit – the more specific binding and fewer false positives a probe set has, the higher our sensitivity and dynamic range can be.

From these questions, it’s clear researchers are thinking deeply about the ways they can leverage our platform to answer new questions about biology. We are excited to work in this under explored area.

Broadscale proteomics and confident protein measurements

In proteomics there has been a trend toward reporting ever-increasing numbers of protein identifications. We have designed our platform to measure substantively the entire proteome in a single experiment, but perhaps more importantly, we have also designed it to provide high quality measurements across the proteome and give researchers confidence in their data. 

In the broadscale section of our lunch seminar, we focused on the many ways we’ve designed the Nautilus Platform to produce high quality data. Key to this quality, is the iterative measurement of intact single protein molecules. Walking through our Protein Identification by Short-epitope Mapping (PrISM) methodology for quantifying intact proteins at the single-molecule level, Nautilus Co-Founder and Chief Scientist Parag Mallick stressed that we identify proteins by independently probing each single protein molecule with many multi-affinity reagents. These many probe binding events lead to very high-confidence protein identifications. These stand in contrast to identifications on other platforms where there may be only one or two touches on a protein when making a call.   

Questions in this section focused on various aspects of data quality and included:

• How many times can we probe isolated protein molecules before data quality degenerates?
  We’ve demonstrated hundreds of cycles of probe binding with high stability and limited variability in output. 
• How do we achieve high dynamic range?
  We’ve designed our flow cells to accommodate up to 10-billion proteins and because our protein identification methods don’t degrade with decreased protein abundance (proteins are identified by patterns of multi-affinity probe binding to single protein molecules), we anticipate being able to quantify substantively the entire proteome even if there are trillions of proteins in a sample. The sheer size of our flow cells, our single-molecule identification method, and our well-characterized multi-affinity reagents combine to give us the sampling statistics needed to quantify proteomes of this size. 
• Is there bias in your sample prep?
  Leveraging universal protein standards, we’ve shown there is little bias from our sample prep. We get the same mixture of proteins out as we put in.

As with the section focused on targeted proteoform studies, the questions showed that researchers are thinking carefully about how they’re going to use our platform. We were proud to answer such detailed questions and highlight the high-quality data we aim to generate.

Access our US HUPO presentation showing how we robustly characterize our multi-affinity reagents 

Palpable excitement for Nautilus 

Nautilus Senior Director of Scientific Affairs and Alliance Management, Andreas Huhmer similarly shared that people who visited his poster asked more in-depth questions and seemed more excited about our proteoform assay than they’d been in the past. More than asking about the basics of our technology, they were intrigued to learn how they could leverage our platform in their own work. Others wondered how targeted proteoform studies would change Alzheimer’s research – definite signs that people are thinking deeply about the ways Nautilus can change biology.

We love and appreciate the support from this fantastic community and cannot wait to share more data from the platform in the coming months!

Listen to Parag Mallick, Ben Neely, and Ben Orsburn discuss science communication and proteomics on Translating Proteomics