Proteomics is still a relatively young field of research that looks at the entirety of all proteins (proteome) and tries to find out which proteins are present in the cells, what functions they have, and how they interact. Our entire body is made up of thousands of different proteins. And enzymes, which are also made of proteins, regulate important metabolic processes.
With the help of proteomics, we can create a kind of huge library in which proteins are classified and organized. This gives us a better understanding of the relationships in our body and allows us to understand which processes are disrupted in diseases or how medications affect the body.We explain to you in this article clearly what proteomics is, what it has to do with epigenetics, and how we can use this technique.
What is proteomics?
In plain terms, proteomics is the comprehensive study and analysis of the proteome, which is the entirety of all proteins expressed in a cell, tissue, organism, or specific biological system at a given time. It deals with the identification, quantification, structure, function, and interactions of proteins as well as their changes under different conditions.
Through the use of advanced technologies, such as mass spectrometry and bioinformatics tools, proteomics aims to gain a detailed understanding of the role of proteins in biological processes and diseases and thus significantly contributes to the development of new diagnostic methods, therapies, and the understanding of disease mechanisms.
The proteome as the wardrobe of your life
Proteomics – can it be explained more clearly?
Admittedly, the complex backgrounds of proteomics are not entirely easy to explain. In our article about epigenetics we compared it to the volume controls .For proteomics, we can draw another analogy: a wardrobe. Imagine your wardrobe is packed full of different clothing items, each serving a specific function. Each clothing item represents a protein in your body, and the totality of all proteins (or your wardrobe) is referred to as the proteome. Similar to a wardrobe, the proteome can be diverse, with a wide variety of proteins responsible for different cellular functions and processes. Some proteins are like your favorite clothing items that you wear often and play an important role in your daily life. Here one would speak of essential proteins .
Other proteins are like the rarely worn or seasonal clothing items that are only needed for certain occasions.
The wardrobe of life
Just as you organize your closet according to your needs and select certain clothing items that match your style, your body regulates the expression and activity of various proteins according to the demands and conditions. This process is called proteomics and involves the study and analysis of all proteins in a cell, tissue, or organism at a specific point in time.
For example, when you train, your body can produce proteins that are important for muscle recovery and the building of new muscle mass. These proteins are activated to meet the specific demands of your training. Just as you might choose your sportswear to prepare for your workout, your body selects specific proteins to enable the physiological adaptations to training.
Proteomics allows us to investigate the complex interplay of proteins in biological systems and understand how they respond to various environmental factors, diseases, or therapeutic interventions. By analyzing the proteome, we can gain insights into the functioning of cells and tissues and discover new opportunities for the diagnosis, treatment, and prevention of diseases. We investigate, to stay with the analogy, which "garments" are used in which life situations.
Why use proteomics?
Proteomics offers a kind of "live insight" into the cell. With genetics, we have so far been able to make the blueprints visible "only." Through proteomics, it is now possible to gain a new perspective. We can see whether proteins are modified again after their translation, z.B. through phosphorylations or glycosylations. This means we get a more detailed insight into the processes of the cell. This way, researchers can also better study protein-protein interactions and thus better understand complex biological signaling pathways.
What advantages does proteomics offer?
Proteomics is the next step towards more personalized medicine. Through research efforts, it may be possible in the future to better identify new biomarkers for diseases or therapeutic target molecules. Additionally, with the help of proteomics, we can enhance our understanding of how medications affect the body.
Research is still relatively in its early stages, but there are already some very exciting studies. In this study , 36 individuals with different backgrounds were tested before and after exercise. The analyses were extremely comprehensive, ranging from blood tests to proteome and gene analyses.The researchers were able to determine that some proteins serve as markers for later performance in endurance tests. They also found that people with insulin resistance show a changed response to exercise. Before deriving precise treatment approaches from this, a bit more research needs to be done, but the results are already extremely exciting so far.
How do you measure proteins?
There are various methods to measure proteins. For proteomics, a mass spectrometer is of great importance. But how does such a device work?
A mass spectrometer is like a sophisticated scale that sorts tiny particles like proteins or peptides (short protein segments) by their weight.Imagine you have a bag of differently sized balls and want to sort them by size. A mass spectrometer essentially does the same thing, but with molecules. To give you a better idea of the process behind it, we have illustrated the individual steps as simply as possible:
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Step 1: Sample Preparation
First, the proteins are extracted from a cell or tissue sample. Since proteins are too large and complex to be analyzed directly, they are "broken down" into smaller parts called peptides through a process called digestion (similar to eating).
Step 2: Ionization
The peptides are then fed into the mass spectrometer, where they are ionized. This means that the peptides are electrically charged, similar to when you rub balloons on your hair and they then "stick" to the wall.
Step 3: Flight through the Mass Spectrometer
The charged peptides are sent through the mass spectrometer. The device uses electric fields to accelerate the peptides. The lighter a peptide is, the faster it moves through the device. It's like blowing different sizes of balls through a wind tunnel; the smaller ones fly faster than the larger ones.
Step 4: Detection
At the end of the "flight," the peptides arrive at a detector. The detector measures how quickly each peptide arrived, which indicates its weight (more precisely, the mass-to-charge ratio).This information is presented in a spectrum that looks like a mountain diagram, with peaks corresponding to different peptides.
Step 5: Data Analysis
The collected data – the mass spectrum – is compared with a database that contains information about known peptides and proteins. Through this comparison, scientists can find out, which proteins were present in the sample and in what quantity.
A mass spectrometer works like a very precise scale that breaks proteins into smaller parts, electrically charges these parts, then lets them fly through a device and measures how fast they move. This information helps us understand which proteins are present in a cell or tissue and how they function.
Conclusion on Proteomics
Proteomics is still a relatively young field of research. One of the first papers on this topic was published in 2000 in the prestigious Lancet Journal under the title: “Proteomics: new perspectives, new biomedical opportunities”.
Since then, there has been significant progress in research. The methods have become increasingly sophisticated and cheaper, allowing for larger-scale exploration of proteomics. With the help of Artificial Intelligence (AI), science can better analyze the vast amounts of data and thus discover new biomarkers or develop new therapies with the help of proteomics.
