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Published: 2024-04-09 Updated: 2024-04-10, 08:50

Proteomics – a powerful discovery tool

NEWS Proteomics is the study of the interactions, function, composition, and structures of proteins and their cellular activities.  In the frame of the SciLifeLab Site Umeå / KBC Infrastructure Seminar Series, André Mateus entered the stage to tell us everything you ever wanted to know about proteomics, but never dared to ask.

We dared to ask André five questions.

What is the proteome and proteomics?

“The proteome is the collection of all proteins in a biological sample, which can be for example cells, a tissue, or some biological fluids.“

“Proteomics is the set of tools that are used to study these proteins. It can be just identifying the proteins that are in the sample, but it can also be about quantifying proteins across conditions, such as cancer versus healthy tissue. Proteomics can also be used to measure post-translational modifications, protein turnover, or help in structure biology approaches to determine the three dimensional structure of a protein. “

Which method do you use?

“In my lab, we use what is termed bottom-up proteomics in which proteins are digested into peptides before the analysis. For the analysis of these peptides, we use liquid chromatography coupled to mass spectrometry. The role of liquid chromatography is to separate the complex peptide mixtures that originate from the full proteome of an organism, and the mass spectrometer identifies and quantifies these peptides. “

What do you use proteomics for?

“We are interested in understanding the function of proteins from gut microbiome species, in particular what are the targets of drugs and which proteins are used to metabolize complex carbohydrates (that is, fibres from our diet). “

“For this, we treat representative species of our microbiome with different drugs (particularly non-antibiotic drugs that are used for human targets), or we feed them different carbohydrates. We measure the impact of these perturbations on the proteome. Our hypothesis is that proteins that are important to respond to the drug or to consume the carbohydrate will change in their levels. This provides a starting point to understand the function of these proteins with more traditional biochemistry approaches. “

How did you get involved in this field?

“I was exposed to proteomics during my PhD studies, but only started using it during my postdoc at EMBL in Mikhail Savitski’s lab. During my postdoc I mostly focused on model organisms, like E. coli, but it allowed me to develop the tools that we use now.“

What is the future for a proteomics infrastructure platform in Umeå?

“At the moment we are focused on our research programme, but we are generally happy to collaborate with different groups, if we have the capacity. There are multiple facilities for proteomics in Sweden, but I hope that in the next few years we could re-establish a proteomics facility here at Umeå University. I believe that a close contact with the groups having the samples would speed up the turnaround of results, and facilitate communication with the collaborators. “

For more information, please contact:

Andre Mateus
Assistant professor, other position