New research equipment enables the view of the entirety of proteins within the cell

They are working with the new size (from left to right): Junior Professor Dr. Timo Mühlhaus, Dr. Markus Räschle, Professor Dr. Michael Schroda, Dr. Frederik Sommer, and Professor Dr. Zuzana Storchová. (Photo: Koziel/TUK)

Proteins fulfill many functions in our cells: they are involved in metabolic pathways, regulate nutrient transport, or act as signaling molecules. With the help of mass spectrometers, it is now possible to determine the entire set of proteins, the proteome, of a cell. This technique is also used at the Technical University of Kaiserslautern (TUK). For a new, highly sensitive, and high-resolution mass spectrometer, the federal government and the state of Rhineland-Palatinate provided around 800,000 euros. The device helps to better understand the role of specific proteins in various diseases such as cancer, for example, to develop new therapies.

In a cell, there is a multitude of different molecules, such as proteins. It is estimated that 6,000 to 7,000 different proteins are active in a human cell. Thanks to the latest techniques, it is possible to quantify them precisely. At TUK, Professor Dr. Zuzana Storchová is engaged in this field. She has been researching in this area for a long time. Among other collaborations, she worked with the renowned Munich-based protein expert Professor Matthias Mann and other colleagues in 2012 to investigate for the first time what effects occur in cells when individual chromosomes are present in increased numbers. Healthy human cells have a double set of chromosomes with 23 pairs. In cancer cells, for example, different sets are often found. The team investigated how an excess of genetic material changes the amount of proteins.

"Such work helps us understand which protein has altered function in which disease. Therefore, it is also important to compare the proteomes of healthy and diseased cells," says Storchová, who researches in the Department of Molecular Genetics.

With the new generation of mass spectrometers, this is now possible. "We can analyze almost all proteins of a cell simultaneously," she continues. In this technique, protein molecules are identified and quantified based on their mass. Essentially, they are weighed. Similar to a fingerprint, each molecule has a characteristic value.

The team around Storchová and her researcher colleague Dr. Markus Räßle is also investigating how the proteome in cancer cells differs from that in healthy cells. "We want to understand why certain proteins occur more frequently or less often," says the professor. With the new device, they can more easily identify such key proteins. Understanding these fundamentals is important for developing new or better therapies in the future.

The new research device is located on the Kaiserslautern campus in the Center for Mass Spectrometry Analytics. It is led by Professor Dr. Michael Schroda from the Department of Biotechnology and Systems Biology, together with Professor Storchová. They are supported in conducting the highly complex experiments by Dr. Frederik Sommer and Dr. Markus Räßle. The bioinformatics analysis of the data is handled by the group of Junior Professor Dr. Timo Mühlhaus. The laboratory is also open to research groups from other disciplines such as chemistry. With the mass spectrometer, not only proteins but also other molecules such as lipids can be studied.