Proteomics core facility

The connection of separation power and reproducibility of liquid chromatography with accuracy and sensitivity of mass spectrometry allowed the fast development of the proteomics in the past and still is considered as the standard approach in the current proteomics. After decades of development, LC-MS proteomics is currently extremely sensitive and accurate method allowing to identify and semi-quantify thousands of proteins from cells or tissues and hundreds of proteins from body fluids. At IMTM’s proteomic core facility we offer established LC-MS protocols verified by many publications, regularly checked by stringent quality control. The traditional approach of protein identifications is called data-dependent acquisition (DDA) and is the method of choice in the characterization of the unknown sample.

For the analysis of the higher amount of similar samples, there could be used with benefit another approach, data-independent acquisition. This approach brings better coverage and quantification of the samples, because of the different algorithms comparing directly the obtained mass spectra of all samples and comparing to the central library.  At the IMTM’s proteomic core facility, we have the state-of-art analytic and software tools for this kind of higher throughput analyses.

Targeted proteomics trades off the identification power for the high throughput. The targeted proteomics is the best method for the analysis of known proteins in the bigger sets of samples. At the IMTM’s proteomic core facility, we can offer targeted protocols using traditional Q-trap or Q-TOF instruments as well as using next-generation Thermo SureQuant assay.

The kinase assays offered by IMTM’s proteomic core facility allow to monitor kinase kinetics or inhibitors by targeted MS analysis of nascent and phosphorylated substrate. This assay is high-throughput, optimized for fast inhibitor screening.

For the protein identification from electrophoretic bands or spots, we can still provide traditional MALDI-TOF based protein mass fingerprinting. Compared to LC-MS, MALDI-TOF based identifications allows faster analysis of the proteins of interest with reasonable throughput. This method is suitable to single proteins purified by electrophoresis or the other method, but for the protein mixtures we can offer better methods. 

The Luminex multiplex immunoassay can identify and quantify up to 100 proteins, cytokines or nucleic acids from very small amount of biological material at once. This system is very versatile and can provide fast and cost-effective results. Because the Luminex assay is based on immunoassays, it allows to use the benefit of 96-well plates and analyze with high throughput. 

Development of custom analytical approaches for specific tasks using liquid chromatography and mass spectrometry, mainly in the field of biomolecules analysis.

The current proteomic technologies allow to identify and quantify thousands of proteins and their variants. In typical proteomic experiment, there are compared two or more conditions. Those conditions usually manifest with changes in abundance of particular proteins. Nowadays, there are identified not only the single differentially regulated proteins, but rather the complex pathways. Processing of this kind of data could be very challenging and our team of bioinformatics experts can help with any issue regarding computational processing and bioinformatic evaluation of proteomic results. 

The highly experienced staff on the IMTM’s proteomic core facility can be more than helpful in the design and proper training in the experiments requiring proteome analysis at any point of biomedical research.