The proteomics facility (www.medicalproteomics.com) has been established as part of the Groningen Genomics Centre and is supported by MIBITON, the EU (FP5) and ZON-MW. The facility is also part of the Netherlands Proteomics Centre. The NPC is a strategic collaboration of research groups from six universities, three academic medical centres and several biotech companies. It enables the use of proteomics equipment and expertise of other members of the NPC. The activities of the proteomics facility are performed in close collaboration with prof. dr. R. Jansen of the Groningen Bioinformatics Centre. Furthermore there is close cooperation with Dr. Andries Bruins from the mass spectrometry lab of Pharmacy and with Prof. Dr. Rainer Bischoff, head of the bio-analyses research group of the Department of Pharmacy. The facility is equipped with a range of mass spectrometers enabling LC-MS, Matrix assisted laser desorption and ionization (MALDI) and Surface Enhanced Laser Desorption and Ionization (SELDI).
The activities of the proteomics group are mainly focused on the discovery of protein markers (biomarkers) for diagnosis, to follow disease progression and to monitor intervention effectivity. To find these biomarkers the protein composition of serum, urine or other biofluids of a group of patients is compared with that of healthy controls. For this we make use of SELDI proteinchip technology. This technology has a high sample throughput and is most sensitive in the low molecular weight region where most biomarkers can be found. The technology makes use of proteinchips with different absorptive surfaces such as anion exchange, cation exchange and reversed phase that can bind a certain class of proteins (see figure). In this way the complexity of the sample decreases which enables a more sensitive detection. Detection of the masses of these proteins takes place in a time-of-flight mass spectrometer. With specific bioinformatics software protein profiles of the different groups (disease and control) can be compared to look for statistical differences in the protein pattern. The observed differences can be potential biomarkers and will be further analyzed. To learn more about the (metabolic) function of the discovered biomarkers the identity of the protein needs to be established by purifying the protein and digest it with trypsin. This gives a specific peptide pattern that can be used in a database search to identify the protein (peptide fingerprinting) but can also be used to determine the amino acid sequence with a tandem mass spectrometer (QSTAR XL). The QSTAR is equipped with interfaces for LC-MS/MS, MALDI-MS/MS and SELDI-MS/MS. Peptides can be isolated and fragmented. From the masses of the fragments the amino acid sequence can be deduced or can be used in a database search.