Frequently Asked Questions (FAQ)- Proteomics

Frequently Asked Questions (FAQ)- Proteomics

Q: What is proteomics?
A: Proteomics is the study of the full expression of proteins by cells in their lifetime and is the next major step toward understanding how our bodies work and why we fall victim to disease. It aims to study directly the role and function of proteins in tissues and cells and promises to bridge the gap between genome nucleotide sequences and cellular behavior. Proteomics combines know-how in biology, engineering, chemistry and bioinformatics with technologies that include automation, robotics and integrated systems. Two distinct but complementary strategies have arisen in proteomics – the first monitors the expression of a large number of proteins within a cell or a tissue and follows how this pattern of expression changes under different circumstances, for example in the presence of a drug or in a diseased tissue; the second identifies the structure of proteins and, in particular, characterises proteins that interact with each other. The second approach is suited to the detailed study of particular pathways working in cells; the first offers a broader picture of the proteome. Both will be indispensable tools for drug development.

Proteomics is the study of total protein complements, proteomes, e.g. from a given tissue or cell type. Nowadays proteomics can be divided into classical and functional proteomics.

Classical proteomics is focused on studying complete proteomes, e.g. from two differentially treated cell lines, whereas functional proteomics studies more limited protein sets. Classical proteome analyses are usually carried out by using two-dimensional gel electrophoresis (2-DE) for protein separation followed by protein identification by mass spectrometry (MS) and database searches.

The functional proteomics approach uses a subset of proteins isolated from the starting material, e.g. with an affinity-based method. This protein subset can then be separated by using normal SDS-PAGE or by 2-DE. Proteome analysis is complementary to DNA microarray technology: with the proteomics approach it is possible to study changes in protein expression levels and also protein-protein interactions and post-translational modifications.

Q: What are the applications of proteomics?
A: The main applications of proteomics are in drug discovery (identification of drug targets, target validation, toxicology) and in clinical diagnostics (screening of patients for drug responsiveness and side effects).
Proteomics makes it possible to obtain and rapidly sort large quantities of biological data from the analysis of biological fluids from healthy and sick individuals. This should allow improved diagnostic methods that may be used to identify molecular abnormalities in diseased states.

Q: What are the key bottlenecks in proteomics?
A: Key bottlenecks exist in the current methods used for proteomics research. The sensitivity (for example difficulties in detecting unknown, low-abundant proteins that could be interesting drug targets), reproducibility (lack of standardized methods for two-dimensional electrophoresis) and the high throughput capacity (lack of automation) of all the current methods employed will have to be significantly improved to fulfill the potential of the technologies.

Q: What is the total available market in proteomics?
A: The global proteomics market was valued at $24,361million in 2017, and is expected to reach $72,444 million by 2025, growing at a CAGR of 14.5% during the forecast period.

Q. Can you tell us more about proteomics, which I understand is a relatively new term?
A: The more recent developments in recombinant DNA technologies and other biological techniques have endowed scientists with the unprecedented power of expressing proteins in large quantities, in a variety of conditions, and in manipulating their structures. While scientists were usually accustomed to studying proteins one at a time, proteomics represents a comprehensive approach to studying the total proteomes of different organisms. Thus, proteomics is not just about identification of proteins in complex biological systems, a huge task in itself, but also about their quantitative proportions, biological activities, localization in the living cells and their small compartments, interactions of proteins with each other and with other biomolecules. And ultimately, their functions. Because even the lower organisms can feature many thousands of proteins, proteomics-related activities are likely to keep us busy for two or three decades.

Q.  What is the connection in proteomics between biology and chemistry?
A: With the boundaries between traditional scientific disciplines blurring all the time, this is somewhat difficult to answer. While proteomics has some clear connections to modern biological research, its current research tools and methodologies are chemical, some might even say, physio-chemical. You prominently see there are large, sophisticated machines like mass spectrometers, which in some parts of the world are still considered within the ‘physics domain.’ But things are continuously changing in this dynamic field. Genomic research, a distinct area of modern biology, has significantly changed the way in which we view the task of various proteomes.

Q. What has changed in the past five or so years?
A: The field of genomics, with its major emphasis on sequencing the basic building blocks of the ‘central molecule,’ DNA, already has yielded highly significant information on the previously unknown secrets of living cells. The stories of newly discovered genotype phenotype relationships and strategies for understanding genetic traits and genetic diseases now regularly flood top scientific journals and popular literature alike. In parallel with providing the blueprint of the human genome, the genomes of many bacterial species, yeast and fruit flies for instance, have been sequenced, providing a valuable resource for modern biomedical research. The mouse genome also has been completed recently. Likewise, in the area of plant sciences, some important genomic advances have been reported. Yet, only a part of genetic information is of a direct use to proteomics.

Q. What are some practical applications of proteomics research?
A: Due to the multilateral importance of proteins in living systems, the scope of biomedical application is apparently wide. In fine-tuned functioning of the human body, various proteins act as the catalysts of chemical reactions, cell growth mediators, molecular transporters and receptors, immune agents against microorganisms and more. Consequently, various human diseases manifest themselves in the altered concentrations or structures of proteins, so that finding protein markers of a disease can, for example, result in devising better means of diagnosis or follow-up therapy. Numerous proteins have now been used therapeutically, so that there have to be perfect ways of manufacturing quality control for such therapeutics, or even to trace their action in the human body. Pharmaceutical companies, thus, have considerable interest in proteomics. Various activities in this area also provide considerable stimulus to the instrument industry. Consequently, coming up with new ways and better means to analyze complex protein mixtures is a high priority. These are just a few examples of how proteomics can impact our future.