Proteomics Core Facility

• Practical experience and understanding of all stages of proteomic and chemoproteomic workflows (experiment design, generation of biological samples, sample prep, data acquisition, qualitative and quantitative analysis on peptide and protein level, gene ontology annotation and pathway analysis, data visualisation, report generation)


• Considerable experience in proteomic and chemoproteomic method development and adaptation


• Comprehensive knowledge of software environments and bioinformatics platforms for proteomics data processing and analysis


• Daily communication with individuals and multidisciplinary teams of scientists (consultations)


• Extensive experience in communicating knowledge (delivering seminars and lectures at international meetings, organising and leading sample prep and data analysis workshops)


• Management and motivation skills (supervision of PhD and MSc students as well as research technicians)

• Skills in 2D gel electrophoresis and HPLC with fraction collection techniques as preparation methods for proteomic experiments with mass spectrometry as detection method


• Know-how about uncommon protein samples purification and concentration, methods especially dedicated to be usable with whole blood, tear fluid, urine, saliva


• Skills to managing experiments in a field of tissue imaging, top-down and bottom-up experiments with successfully data interpretation

nLC-coupled Q-Exactive HF-X

• This hybrid quadrupole-orbitrap instrument constitutes a high-performance platform for both bottom-up and top-down proteomics studies. Advanced scanning modes featuring improved peak-picking and the new ultrafast MS/MS scan time below 20 milliseconds yield great improvements in polypeptide sequencing speed and depth.


• Bottom-up proteomics utilizes digestion of proteins into peptides which are then sequenced in the mass spectrometer and act as surrogates for the presence of proteins from which they are derived. Besides insights into protein expression levels and the extent of posttranslational modifications, this mode of analysis can be applied to provide information about protein turnover, subcellular localization, as well as protein-protein and protein-small molecule interactions.


• During top-down proteomics full length proteins are measured and fragmented in the gas phase to deliver information about the amino acid sequence and modifications covalently attached to them. Proteoform-level resolution is achieved by this mode of analysis.

UPLC-coupled Q-Exactive UHMR

• This hybrid quadrupole-orbitrap provides the unique combination of ultra-high mass range resolution, highest sensitivity, and tandem mass spectrometry capabilities to enable unprecedented advancements in native MS and top-down analysis.


• During native MS measurements entire macromolecular assemblies are measured in high resolution to deliver population level quantitative information, elements of these assemblies can be then dissociated to yield further information supporting their identity. This mode of analysis can provide structural characterization (heterogeneity, stoichiometry, non-covalent ligand binding) of soluble and membrane protein complexes as well as megaDalton protein nucleic acid complexes, e.g. ribosomal assemblies or viral particles.


• This instrument can be also utilized for routine screening of purity/homogeneity of Cryo-EM samples and for obtaining complementary structural data. Information on how to access the 200 kV cryo-EM instrument microscope @CeNT are available at CRYO-TEM section.