In recent years, thanks to groundbreaking expansions in genome sequencing, science has documented an unprecedented number of protein sequences. However, a vast portion of these sequences still cloak their functions in mystery. Unraveling such enigmas forms the bedrock of a burgeoning field known as functional proteomics. Particularly pressing is the case of RNA viruses, notorious for causing pandemics with high morbidity and mortality. An insightful chapter within the renowned journal “Advances in Protein Chemistry and Structural Biology,” which was published in 2024 discusses the application of functional proteomics in understanding RNA virus-mediated infections, offering invaluable perspectives that may pave the way for novel antiviral strategies.

The Cutting Edge of Functional Proteomics

As the chapter by Panda Mamta and colleagues deftly outlines, functional proteomics aspires to elucidate the biological functions of unidentified proteins and dissect cellular systems at a molecular scale. RNA viruses are particularly intriguing subjects for this science, as they are known for hijacking host cellular machinery to perpetuate their life cycle. It is within this context that high-throughput sequencing and genetic-based screening technologies have shed light on bewildering aspects of RNA virus replication and pathogenesis.

Disruptive Viruses and the Cellular Havoc

Viruses, by their very nature, are experts at commandeering host cell activities. They dismantle cellular proteostasis, tamper with the structure and stoichiometry of macromolecular complexes, and orchestrate post-translational modifications to bend the cell’s will to their needs. It is therefore imperative for science to closely monitor these alterations—not merely the proteins themselves but their various proteoforms (different molecular forms that a single protein can take), a task where mass spectrometry (MS) stands out with its high precision.

Mass Spectrometry: A Beacon of Hope

With its ability to identify stoichiometry and offer mechanistic insights into cellular and viral protein complexes, MS has become an indispensable asset in functional proteomics. The chapter highlights how MS can accelerate the discovery of antiviral targets by dissecting the intricate interactions between viruses and their hosts.

Solid Bonds: Affinity-based Methods

Unveiling the molecular camaraderie within cells, affinity-based methods are employed to pinpoint interacting proteins within stable complexes, offering strong clues about a protein’s biological role. The relationships of these proteins within certain complexes that engage in specific processes provide scientists with a deeper understanding of both viral tactics and host defenses.

Towards Antiviral Innovation

The integration of various functional proteomics techniques has borne fruit in deciphering the host responses to RNA viral infections. A pivotal takeaway from the chapter lies in the translational implications of these insights, which Monika Mamta and her team believe could unveil new, concrete antiviral targets.

This news article should resonate with professionals and scholars vested in uncovering the secrets of RNA virus functionality. It not only celebrates the progress of functional proteomics but also beckons further inquiry into the molecular dance between pathogens and their unwilling hosts.


1. Mamta M, Kalita E, Singh S, Rao A, Prajapati VK. (2024). “Application of functional proteomics in understanding RNA virus-mediated infection.” Advances in Protein Chemistry and Structural Biology. doi:10.1016/bs.apcsb.2023.04.004

2. Aebersold R, Mann M. (2016). “Mass spectrometry-based proteomics.” Nature. doi:10.1038/nature21346

3. Gstaiger M, Aebersold R. (2009). “Applying mass spectrometry-based proteomics to genetics, genomics and network biology.” Nature Reviews Genetics. doi:10.1038/nrg2681

4. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. (2015). “The Proliferation of the Proteome.” Molecular Cell. doi:10.1016/j.molcel.2015.03.016

5. Venkatesan S, Rose JD. (2010). “Virus-host interactions: powerful discoveries and therapeutic opportunities.” Biochemical Journal. doi:10.1042/BJ20100369

DOI: 10.1016/bs.apcsb.2023.04.004


1. Functional proteomics
2. RNA virus infection
3. Mass spectrometry proteomics
4. Antiviral target discovery
5. Virus-host interactions

The study of functional proteomics opens up a new frontier in our fight against viral infections, especially those caused by RNA viruses. As tools like mass spectrometry become more sophisticated, the role of proteomics in drug discovery and understanding pathogen-host interactions only grows more crucial. This recent article from “Advances in Protein Chemistry and Structural Biology” is a testimony to the progress being made and the promise functional proteomics holds for future therapeutic interventions.