Very few people think about the billions of cells and proteins in our body in their everyday life. But in DTU's mass spectrometry unit Proteomics Core—a platform for analysing proteins—researchers focus on the content of proteins in every single cell when analysing biological material and tissue sections from patients. Among other sources, the samples come from Rigshospitalet's Department of Pathology, which sends samples from patients with liver, pancreatic, brain, and blood cancer to gain greater insight into the role proteins play in the individual diseases.
"A number of hospitals in Denmark and Norway order analyses of cell samples. One of the things they look at is whether patterns in the protein variation can be used to extract more knowledge from their biobanks, where millions of tissue sections and preparations containing biological material from patients are currently stored," says Marie Vestergaard Lukassen, Facility Manager at Proteomics Core.
The mass spectrometry analyses in Proteomics Core take place in a new building at DTU, where instruments the size of photocopiers and refrigerators are lined up in a laboratory room.
Before the biological samples are placed in the machines, they must be prepared. The protein content of the sample is extracted from cells and tissue and then subjected to a process where the laboratory technicians use a digestive enzyme to break down the proteins. The enzymes act as a kind of chemical scissors that cut the proteins into smaller pieces, making it easier to see which proteins are in the sample and how much of them is present.
Cuts protein into peptides
To perform the analyses, the laboratory technicians take a sample of the proteins and place them in a tube with a digestive enzyme. For larger samples, the mixture is heated and shaken to ensure the enzyme comes into contact with the proteins and starts cutting them into smaller parts. In single-cell mass spectrometry, however, the laboratory technicians work with much smaller amounts of material, and therefore this entire process can take place in a droplet, which does not offer the same physical opportunities to heat and mix.
