Proteins are essential for assembling molecular structures, organizing signaling mechanisms, and executing biological functions within organisms. Changes in protein structure or activity may indicate disease, making their study crucial for early diagnosis and precision medicine.
Download this poster from Drug Discovery News to learn about the proteomics tools that scientists use to discover biomarkers, detect low-abundant proteins, and monitor disease progression.
BY SUNITHA CHARI, PHD ILLUSTRATED BY SHANNON HERRING
For a long time, genomics has been the prominent tool scientists use to understand the biology of diseases. While genetic data associate genes and diseases, the functional unit of a gene is usually a protein that may be involved in a wide range of cellular processes. Altered proteins can lead to phenotypic changes and disease (1).
PROTEOMICS & PRECISION MEDICINE
Proteomics is the large-scale analysis of the proteins present in a sample. By using proteomics approaches, researchers investigate disease-related pathways, identify biomarkers, and study the pattern and progression of disease (1).
PROTEOMIC ANALYSIS TECHNIQUES
Mass spectrometry is the technique of choice for discovery proteomics, which reveals the entire protein complement in a biological sample. Newer affinity-based techniques are used for targeted proteomics methods to investigate a specific group of proteins and monitor their dynamic behavior in a sample (2,3).
MASS SPECTROMETRY
Mass spectrometers detect biomolecules such as proteins, lipids, and carbohydrates by separating ions based on their mass to charge ratios (1,3).
Proteomics studies using mass spectrometers are usually carried out using a “bottom-up” approach wherein scientists digest proteins from a biological sample into smaller peptide fragments using proteases. The peptides are separated using chromatographic methods (1,3).
COMPONENTS OF A MASS SPECTROMETER
All mass spectrometers have three fundamental components: ion source, analyzer, and detector. The peptide fragments are converted into gaseous ions using methods such as electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI). Mass analyzers such as quadrupoles and time-of-flight (TOF) analyzers separate ions by manipulating their paths in an electrical field, and detectors analyze the signal to identify the peptide (1)
MULTIPLEXED ELISA
In this immunoassay, beads coated with different fluorescent dye microparticles are attached to specific capture antibodies. Each colored bead binds a specific part of an antigen that can be measured by flow cytometry (4)
PROXIMITY EXTENSION ASSAY (PEA)
PEA requires the binding of two matched antibodies labeled with complementary oligonucleotides to the protein of interest. The two oligos hybridize due to proximity and are extended by DNA polymerase. Scientists evaluate the initial protein concentration based on the corresponding concentrations of the DNA amplicons (4).
APTAMERS
Aptamers are single-stranded oligonucleotides that bind specific protein molecules. Scientists measure proteins captured by aptamers using DNA microarray (4).
THE POWER OF PROTEOMICS
The power of proteomics lies in the choice of technology used to address the research question. Scientists use mass spectrometry for identifying novel disease-related biomarkers (1). Affinity-based technologies offer high sensitivity for low abundance proteins, but the application is limited to known protein targets (3, 4). Integrated proteomics approaches allow researchers to investigate the role of proteins in health and disease and deliver on the promise of precision medicine.
REFERENCES
1. Sinha, A., Mann, M. A beginner’s guide to mass spectrometry-based proteomics. Biochem (Lond) 42(5), 64-69 (2020).
2. Marx, V. Targeted proteomics. Nat Methods 10, 19–22 (2013).
3. Xie, S., Moya, C., Bilgin, B., Jayaraman, A., Walton, S. P. Emerging affinity-based techniques in proteomics. Expert Rev Proteomics. 6(5), 573-583 (2009).
4. Rojo, A. C. et al. Towards Building a Quantitative Proteomics Toolbox in Precision Medicine:
A Mini-Review. Front Physiol. 12, 723510 (2021).