WCM-Q study probes use of nanoparticles for human protein analysis

Researchers at Weill Cornell Medicine-Qatar (WCM-Q) have published a study demonstrating the use of an advanced nanoparticle-based tool for analyzing human proteins in order to discover both their function and potential drug targets for treating genetic diseases.

The research tool, provided by US biotech firm Seer, Inc., is a pioneer in the field of proteomics – the study of human proteins.

Researchers believe that understanding the role of proteins in a host of human diseases holds the potential to enable the creation of a new generation of protein-targeting therapies, but analyzing the nature of proteins remains technologically problematic, owing to their vast number and complexity. To meet this challenge, researchers at WCM-Q are intensively studying and testing the most advanced protein analysis platforms to discover which of the available tools is most effective. At the same time, the researchers are conducting their own studies of the human proteome – the sum of all human proteins – to identify proteins associated with disease, and also the genes associated with the disease-causing proteins.

The latest WCM-Q study in this field, titled, ‘A genome-wide association study of mass spectrometry proteomics using a nanoparticle enrichment platform', has been published in the leading scientific journal Nature Genetics. Dr. Karsten Suhre, professor of physiology and biophysics at WCM-Q and director of the bioinformatics and virtual metabolomics core, is lead author of the study.

“Gaining a deeper, more complete and more accurate view of the proteome holds the potential to point the way to new therapies for many human diseases,” said Dr. Suhre. “The challenge is that analyzing the proteome is very difficult – the quantity of data is vast, proteins are highly complex and dynamic, and different proteins often have similar structures to one another, making them difficult to identify, distinguish, quantify and analyze. Therefore, we are working with leading biotech companies such as Seer to rigorously test the most cutting-edge proteomics tools to find novel methods for gaining the clearest and most comprehensive view of the human proteome possible.”

Proteomics studies like this one are based upon analysis of large numbers of human tissue samples, whether taken from blood, saliva, or other sources, provided by large-scale biobanks. It is necessary to analyze and compare samples from very large numbers of individuals to positively identify proteins, peptides (the constituent parts of proteins) and genes associated with disease. WCM-Q’s advanced research infrastructure provides the technical expertise and computing power to handle the large amounts of data generated by these studies.

The Proteograph™ Product Suite from Seer Inc. uses nanoparticles which enrich particular proteins, making them easier to isolate and identify. The technology builds on an established method called mass spectrometry, in which molecules are ionized using a high-energy beam of electrons and then separated and identified by their differing atomic masses. The study found that nanoparticle-enriched mass spectrometry can complement the use of another proteomics technology, known as affinity-based proteomics, in which antibodies or other binding molecules are used to detect specific proteins. A key part of proteomics is the quest to identify so-called ‘protein quantitative trait loci’, which are specific physical regions of the genome associated with variation in protein expression levels. This is important because many diseases, including many extremely debilitating inherited diseases, are caused by genetic mutations which in turn cause dysfunctional expression of specific proteins.

Dr. Frank Schmidt, professor of biochemistry and biophysics, and director of the proteomics core at WCM-Q, said: “This study demonstrates that in our work to map the proteome, to understand how it works, and to discover associations between specific genes, proteins and diseases, it is beneficial to use a number of proteomics platforms in a complementary fashion. These discoveries, and the establishment of a very advanced proteomics infrastructure in Qatar, are helping to place WCM-Q and Qatar among the global leaders in proteomics research.”

The paper can be read in full here: https://www.nature.com/articles/s41588-025-02413-w

This study was supported by the Biomedical Research Program at WCM-Q, a program funded by the Qatar Foundation. Dr. Karsten Suhre is also supported by Qatar National Research Fund (grant nos. NPRP11C-0115-180010 and ARG01-0420-230007) and the Qatar Research, Development and Innovation Council.