Exploring India's emerging role in the large-scale study of proteins and its implications for medicine and biotechnology
While the Human Genome Project captured global headlines by sequencing our DNA, a quieter, more complex revolution was brewing in laboratories. Scientists realized that knowing the blueprint of life was just the first step. The true actors in the drama of biology are proteins—the versatile molecules that build our structures, digest our food, fight our infections, and orchestrate our cellular processes. This realization gave birth to proteomics, the large-scale study of all proteins an organism produces 3 .
In India, this field has experienced remarkable growth over the past decade, positioning the country as an emerging leader in global proteomics research 4 . From Bangalore to Delhi, Hyderabad to Kolkata, Indian scientists are harnessing cutting-edge technologies to decode disease mechanisms, discover new biomarkers, and develop innovative diagnostic tools tailored to the unique needs of diverse populations. This article explores India's journey in proteomics, the groundbreaking work shaping its future, and how this science is transforming medicine at the molecular level.
While humans have approximately 20,000-25,000 genes, these can generate over a million different protein variants through alternative splicing and modifications.
Proteomics provides a dynamic view of cellular activity that static DNA sequences cannot capture.
India now boasts over 100 research laboratories across approximately 80 institutes dedicated to proteomics.
Proteomics enables discovery of biomarkers for early disease detection and personalized treatments.
India's entry into the proteomics arena began somewhat slowly, but has gained dramatic momentum in recent years. The country now boasts over a hundred research laboratories across approximately 80 academic and research institutes dedicated to proteome-level investigations 4 . This expansion has been fueled by increasing government support, growing infrastructure, and the founding of the Proteomics Society, India (PSI), which provides a crucial platform for knowledge exchange and collaboration 7 .
The Clinical Proteomics Remote Triggering Virtual Laboratory represents another innovative Indian initiative, creating virtual learning platforms that allow students and researchers to gain hands-on proteomics experience remotely 4 . Such educational advances are cultivating the next generation of Indian proteomics researchers, ensuring the field's continued growth.
The Clinical Proteomics Remote Triggering Virtual Laboratory allows students across India to access sophisticated proteomics equipment and training remotely, democratizing access to cutting-edge research tools.
If the genome is the entire cookbook of life, containing all possible recipes, the proteome represents the specific meals being prepared in a kitchen at any given time—dynamic, changing with needs, and far more reflective of what's actually happening biologically 5 . The term "proteome" was coined in 1994 by Marc Wilkins, then a PhD student, as a blend of "protein" and "genome" 3 .
Unlike the relatively static genome, the proteome is in constant flux, changing with time, environmental conditions, and cellular demands 1 3 . While humans have approximately 20,000-25,000 genes, these can generate over a million different "proteoforms" through alternative splicing and post-translational modifications 5 . This complexity makes proteomics both challenging and rich with information.
| Genome | Static blueprint |
| Proteome | Dynamic expression |
| Complexity | ~25,000 genes → 1M+ proteoforms |
Quantifies and identifies differences in protein expression between samples (e.g., healthy vs. diseased tissue) to pinpoint disease-specific proteins 1 .
Maps out the three-dimensional structures of protein complexes to understand their functional mechanisms 1 .
Deciphers protein functions and interaction networks within cells to reveal biological roles and signaling pathways 1 .
Proteomics technologies have evolved significantly from early two-dimensional gel electrophoresis (2DE) developed in 1975 to modern mass spectrometry-based methods 5 . The core approaches include:
| Technique | Principle | Primary Applications |
|---|---|---|
| 2DE Gel Electrophoresis | Separates proteins by charge (1st dimension) and mass (2nd dimension) | Initial protein separation, expression profiling |
| Mass Spectrometry | Measures mass-to-charge ratio of ionized peptides/proteins | Protein identification, quantification, post-translational modification analysis |
| SILAC | Uses stable isotope labeling for quantitative comparison | Cell signaling studies, protein turnover measurements |
| iTRAQ | Employs isobaric tags for multiplexed quantification | Comparative proteomics across multiple samples |
| Protein Microarrays | Immobilizes proteins or antibodies on chip surfaces | High-throughput protein expression profiling, interaction studies |
In 2025, Indian researchers participated in a groundbreaking international study that directly compared eight different proteomics platforms applied to the same set of plasma samples 8 . Plasma presents a particular challenge for proteomics because its protein concentrations span an astonishing 10 orders of magnitude—meaning the most abundant proteins are 10 billion times more concentrated than the scarcest ones, making it difficult to detect low-abundance biomarker proteins without sophisticated technology 8 .
Plasma samples were obtained from 78 individuals (equal sex ratio, including both young and older adults) through plasmapheresis 8 .
Each sample was analyzed using eight different proteomics platforms representing both affinity-based and mass spectrometry methods 8 .
Results were aggregated and compared using UniProt IDs to standardize protein identification across platforms 8 .
The platforms included affinity-based technologies (SomaScan, Olink Explore, NULISA) and mass spectrometry-based approaches (nanoparticle enrichment, high-abundance protein depletion, and targeted quantification) 8 .
The findings revealed both the capabilities and limitations of current technologies:
| Platform | Type | Proteins Detected | Key Strength |
|---|---|---|---|
| SomaScan 11K | Affinity-based (Aptamer) | 9,645 | Broadest coverage |
| SomaScan 7K | Affinity-based (Aptamer) | 6,401 | High precision |
| MS-Nanoparticle | Mass Spectrometry | 5,943 | Deep untargeted profiling |
| Olink Explore 5K | Affinity-based (Antibody) | 5,416 | High specificity |
| MS-HAP Depletion | Mass Spectrometry | 3,575 | Standard discovery approach |
| Olink Explore 3K | Affinity-based (Antibody) | 2,925 | Targeted profiling |
| MS-IS Targeted | Mass Spectrometry | 551 | Absolute quantification |
| NULISA | Affinity-based | 325 | High sensitivity |
This research demonstrated that method choice significantly impacts biological conclusions—a critical consideration for Indian researchers designing studies on limited budgets. The technological comparison provides a valuable decision-making resource for selecting appropriate platforms based on specific research goals 8 .
Proteomics research relies on a sophisticated array of reagents and materials designed to handle the complexity of protein analysis. Here are some key components of the Indian proteomics researcher's toolkit:
| Reagent/Material | Function | Application Example |
|---|---|---|
| Trypsin | Enzyme that digests proteins into smaller peptides | Sample preparation for mass spectrometry |
| SILAC Media | Contains stable isotope-labeled amino acids for metabolic labeling | Quantitative proteomics using cell culture |
| iTRAQ Tags | Isobaric chemical tags for multiplexed protein quantification | Comparing protein expression across 4-8 samples simultaneously |
| Antibodies | Bind specifically to target proteins or modified residues | Western blotting, immunoassays, protein microarrays |
| SOMAmers | Modified aptamers that bind specific protein targets | SomaScan platform for affinity-based proteomics |
| Nanoparticles | Enrich low-abundance proteins through surface interactions | Plasma proteomics using Seer Proteograph platform |
| LC Columns | Separate peptides by hydrophobicity before mass spectrometry | Liquid chromatography-mass spectrometry (LC-MS) |
| Anticoagulants | Prevent blood clotting during plasma preparation | Blood sample collection for clinical proteomics |
Proper sample preparation is critical in proteomics. Indian labs have developed optimized protocols for:
Indian bioinformatics teams work with specialized software for:
Indian proteomics stands at an exciting crossroads. The integration of artificial intelligence with proteomics data analysis is already underway, with upcoming symposiums focused on "Harnessing Artificial Intelligence for Multi-Omics Data Integration and Analysis" 7 . These computational approaches will help extract more meaningful biological insights from the complex datasets generated by proteomics studies.
The next generation of proteomics technologies promises to reveal even more of the proteome. While current methods typically identify less than 10-30% of proteins in a sample, emerging platforms aim to measure over 95% of the proteome 9 . Such advances would dramatically accelerate biomarker discovery and drug development.
India's particular strengths in information technology, biotechnology, and traditional medicine knowledge position it uniquely to contribute to global proteomics advances. As infrastructure continues to improve and international collaborations expand, Indian researchers are poised to make increasingly significant contributions to our understanding of the human proteome and its implications for health and disease.
Machine learning algorithms will enhance protein identification, quantification, and functional annotation from complex proteomics datasets.
Emerging technologies will enable protein analysis at single-cell resolution, revealing cellular heterogeneity in tissues and tumors.
Combining proteomics with genomics, transcriptomics, and metabolomics will provide comprehensive views of biological systems.
India's strengths in information technology, biotechnology, and traditional medicine knowledge position it uniquely to contribute to global proteomics advances. The combination of technical expertise, diverse population genetics, and cost-effective innovation creates ideal conditions for breakthroughs in personalized medicine and biomarker discovery.
Proteomics represents more than just a technical advancement—it offers a fundamentally deeper understanding of life's processes. In India, the growth of this field mirrors the country's broader scientific development, demonstrating how strategic investment in research infrastructure and education can yield dramatic returns.
As Indian researchers continue to innovate in proteomics, the potential benefits extend far beyond laboratory walls. From early disease detection to personalized treatments and improved public health outcomes, the proteomics revolution promises to translate molecular insights into tangible human benefits. The work happening today in laboratories across India will help write the next chapter of this exciting scientific story, proving that sometimes the most profound discoveries come from studying the smallest pieces of ourselves.