Proteomics Core Facility

The mission of the Proteomics Core Facility is to provide an analytic platform and to couple it to users' research interests. The core facility is a state-of-the-art mass spectrometry lab equipped with top-level instrumentation, complemented by expertise ranging from sample preparation strategies, through mass spectrometry (MS) to computational proteomics. Given the highly technological nature of this approach, the facility's primary focus is on analytic instrumentation and methodology. However, to bring the technology closer to scientific users, we also focus on instruction, consultation and discussion at every stage of a project. Close attention is given to qualityservice, fast reaction times to users' requests and the complete integration of the facility with the scientific objectives of the institute.

  • Tandem Mass Tag (TMT) quantification strategy coupled with high-pH peptide fractionation for maximal analytical depth
  • Interaction proteomics by label-free quantification and Data-dependent acquisitions (DDA)
  • Label-free Data-Independent Acquisition (DIA) for protein quantitation for large sample cohorts
  • Protein digestion using a variety of proteases (trypsin, Lys-C, Glu-C, Asp-N etc.) and approaches (in solution, FASP, in gel)
  • StageTips (C18, SAX, SCX, SDB-RPS, SDB-XC): purification, desalting, fractionation and concentration
  • Off-line Pre-fractionating via HPLC
  • gel electrophoresis, staining and imaging (Gel Doc EZ imager)
  • TMT labeling
  • SP3 sample preparation for detergent-containing samples

Orbitrap Fusion Lumos Tribrid ETD with EASY 1200 UPLC and FAIMS Pro Interface

Orbitrap Fusion Tribrid ETD with EASY 1000 UPLC

Q Exactive HF with EASY 1000 UPLC

  • MaxQuant quantitative proteomics software package
  • Spectronaut
  • Proteome Discoverer
  • Perseus framework
  • Statistical environment R
  • IPA Analysis Match Explore suite