Overview of Proteomics & Proteomics Analysis

In this blog we give an overview of both proteomics and proteomics analysis. We discuss what proteomics is and what its applications are; as well as explaining what proteomics analysis involves and what it can tell us.

Proteomics definition – What is proteomics?

Proteomics refers to the study of the proteome of a biological system such as an organism, tissue or cell. The proteome is the complete set of proteins present in a biological system at a particular time. A cell’s proteome is determined by its genome and environment and often changes to reflect the behaviour of the cell. Since this is the case, we can study proteomes in varying contexts.

How does proteomics work?

You now know that proteomics is the study of a set of proteins (proteome) within a biological system, but what does that mean? What do we want to find out about those proteins?

There are generally three things to uncover;  what is the structure of the proteins? How do they function and how do they interact with each other? However, it is first important to note that proteomes are ever-changing. In fact, the composition of a proteome changes throughout time for a variety of reasons. For example, the proteome can change throughout the life of an organism or in response to both external and internal factors. For this reason, often when researchers refer to a proteome, they are referring to it at a specific point in time.

So, how do we figure out the structure of proteins and how they are functioning and interacting with each other at a given point in time? The short answer is via proteomics analysis using bioinformatics. We explain more about this in the proteomics analysis section later in this article.

What are the types of proteomics?

There are three main types of proteomics; functional proteomics, expression proteomics and structural proteomics.

Functional proteomics investigates the biological function of proteins and examines protein interactions. In particular, it examines the interactions of unknown proteins with known proteins in a particular protein complex.

Expression proteomics studies the expression of proteins, both quantitively and qualitatively. The goal of expression proteomics is to determine the difference in protein expression between two conditions.

Finally, structural proteomics focuses on determining the three-dimensional structure of proteins, specifically proteins that have biological activity (functional proteins).

Researchers use various different technologies in proteomics research and the type of proteomics will often dictate the type of technology used. Common technologies currently used within proteomics include X-ray crystallography, labelled or label-free LC-MS/MS,  nuclear magnetic resonance spectroscopy and protein immunoassays.

What is proteomics used for?

Proteomics has many and varied uses, particularly in medicine. For example, proteomics can support drug development by mapping the protein interactions associated with a particular disease or by indicating the “drugability” of protein targets.  Proteomics can also be used to identify and quantify protein biomarker and PTMs associated with drug response or survival.  In addition, proteomics also plays an important role in cancer research which is why oncoproteomics is a sub-discipline of proteomics. For detailed explanations of the applications of proteomics in terms of protein levels and quantifications etc. there is a useful table in this article from Technology Networks. On the other hand, if you would prefer to learn more about the applications of proteomics in medicine we recommend Proteomics: Concepts and applications in human medicine from the World Journal of Biological Chemistry.

If you work with proteomics or intend to in future, please keep Fios Genomics in mind. As a leading bioinformatics service provider we have over a decade of experience in proteomics analysis. In fact, if you are wondering if or how proteomics data could help you reach your particular research goals, we can draw on our expertise to advise you. Contact us now and we will be happy to answer your proteomics questions.

What are proteomic techniques?

There are many proteomic techniques and they fall into two main categories; high-throughput techniques and low-throughput techniques. Low-throughput methods include gel-based, chromatography-based and antibody based methods. On the other hand, high-throughput methods are usually mass-spectrometry based or array based.

This article from the Journal of Chromatographic Science gives a good overview of the different technologies and their applications. Figure 1 is a particularly helpful overview of the many proteomics technologies currently available.

What is the difference between proteomics and genomics?

Despite being two different fields, proteomics and genomics are closely related. This is why it is important to know the difference between the two.

Whereas genomics focuses on the genome, proteomics focuses on the proteins that an organism produces. Genomics is the study of genomes. A genome is all of an organism’s genetic material and it is comprised of DNA. It contains all of the information necessary to build an organism and for that organism to develop. Most cells within an organism will contain a copy of the organism’s genome.

Proteomics, on the other hand, refers to the study of proteomes and we know that a proteome is comprised of all the proteins within an organism, or within a biological system such as a cell.

Therefore, on a cellular level, genomics studies the genome of a cell (all of the genes contained within the cell) while proteomics studies all of the proteins that the cell produces.

Although the organism’s DNA contains the instructions for producing its proteins, the way that those instructions are read depends on the environment. As such, the proteome can adapt and change over time, whereas the genome is mostly static and it is not possible to fully predict an organism’s proteome from its genome.

Proteomics analysis

Since proteomics studies often generate massive amounts of data, and since there are many different technology platforms which generate proteomics data, proteomics analysis can be complex. Due to the complexity and quantity of the data produced by proteomics, the analysis might require bioinformatics expertise. A bioinformatician will use their computational skills and resources to process vast proteomic datasets and then use their biological knowledge to interpret the results. Bioinformatics might be necessary to get the most out of proteomics analysis; it will also help in getting relevant and meaningful biological insights to help answer your research question.

How is proteomics analysis done?

Since there are so many proteomics technology platforms and so many applications of proteomics data; there are also many different ways to analyse proteomics data. However, most analyses of proteomics data are designed to quantify the changes in protein abundance, modification, location or binding specificity between groups of samples that differ with respect to tissue of origin, treatment, experimental condition or outcome. Proteomics analyses are relevant for a range of applications such as:

• Profiling of proteomes between normal and diseased tissues
• Identification and quantification of protein biomarkers and PTMs associated with drug response or survival
• Identification of direct targets and indirect effects of drugs and other active molecules

Proteomics analysis sample report

If you would like to understand more about how proteomics analysis is done, request our sample report.  Our proteomics analysis sample report describes our analysis of mass spectrometry based proteomics data to identify differences in protein expression levels between four segments of the large intestine: ascending, transverse, descending and sigmoid colon. 

Proteomics for biomarker discovery

It is common to use proteomics for biomarker discovery. At Fios Genomics, we have particular experience in proteomics analyses for this application. We have designed specific analyses to identify and quantify protein biomarkers and PTMs associated with drug response or survival. Also, our bioinformaticians are particularly adept at identifying predictive biomarkers via the correlation of protein levels with patient response to treatment.

Proteomics Data Analysis Service

As a market-leading bioinformatics provider, proteomics analysis is one of our core services. Our wealth of experience in this area allows us to offer a rapid turnaround service for proteomics data. Not only can we analyse proteomics data from numerous platforms; but we can also receive data in various formats for the analysis, such as peptide- or protein-specific intensities and spectral count matrices. To discuss a proteomics project please contact us, we are always happy to share our expertise. Alternatively, to learn more about our proteomics analysis services visit our proteomics data analysis page. There you will find information about our proteomics services and what our proteomics data analysis pipeline includes. Additionally, you will also find details of some of our previous projects in this area.

Fios provide you with a very nice data package, that is fully interpretable and allows you to draw meaningful conclusions.

Dr David Moffat, Director of Chemistry at Macrophage Pharma

Author: Breige McBride, Content and Social Media Manager, Fios Genomics
Reviewed by Fios Genomics Bioinformatics Experts to ensure accuracy

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