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Proteins are essential for the vital functions of the body. They manage most of the cell functions and enable complex interactions between the cell and its environment. The study of proteins can therefore offer extensive information about the different functions of cells. Protein analyses can be utilised broadly in medical research, including gut microbiome profiling.

The important role of the gut microbiota on human health and their role in different diseases has been recognised in studies published over the recent years. A research group from the University of Turku led by Professor Laura Elo has developed a new mass spectrometry-based method, which enables extensive studying of protein levels in complex microbiota samples.

“Until recently, the research on microbiota has strongly focused on discovering which microbes are present in a sample, but analysing the functionality of the microbiota has been challenging. Recent technological advancements have however also enabled a deeper dive into the functionalities. The study of the protein levels in microbiota samples is one such rising research field, making it possible for us to reach a broader understanding of the functionality and dynamics of microbiota,” says Elo.

The recently developed method utilises newest mass spectrometry technology and advanced computational methods which enable significantly better coverage and reproducibility of the results as opposed to previous methods.

“The new method we have developed for analysing complex protein data produces more reliable results than previous methods,” says Postdoctoral Researcher Sami Pietilä.

“The currently used research methods typically only analyse the most abundant proteins, which causes fluctuation in the results from one analysis to another. The new method analyses the samples systematically and produces reliable results without this type of fluctuation,” Pietilä continues.

The computational method has been published as open source software and is freely accessible for the research community.

“It has been extremely important for us to bring this newly developed method available for all researchers as an easy-to-use application. We are also prepared to engage in further development and maintenance of this tool,” adds Postdoctoral Researcher Tomi Suomi.

Pietilä S, Suomi T, Elo LL. Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples. ISME Communications, 2022. https://doi.org/10.1038/s43705-022-00137-0

Press release from University of Turku