The Proteomics Core Facility offers a range of techniques for the identification, characterization and quantification of proteins and proteomes. These include the following techniques and approaches, often used in combination – please enquire for additional applications that may fit your needs.

Protein and Peptide Separation

  • High pH (pH 10) reverse phase chromatography, for offline fraction collection, as a pre-fractionation step in peptide-based proteomics, prior to LC-MS/MS analyses.
  • SDS-PAGE gel electrophoresis.

Protein Digestion and Labeling

  • Protein digestion in-gel or in-solution, using a variety of proteases (trypsin, LysC, chymotrypsin, ArgC, GluC, AspN).
  • In-gel acid hydrolysis for determination of N- /C- termini (eg. for samples from limited proteolysis experiments).
  • Peptide purification using OasisHLB μElution plates (Waters), Sep-Pak C18 cartridges (Waters).
  • Peptide labeling with stable isotopes (TMT, reductive methylation) for relative protein quantification.  In addition, we fully support workflows using SILAC labeling.

Mass Spectrometry: MS, LC-MS and LC-MS/MS

  • Identification of proteins from coomassie stained gels (please see here for MS compatible staining recipe).
  • LC-MS (C4 reverse phase UPLC) for protein molecular weight determination under denaturing conditions.
  • Complex proteome analysis, often combined with additional protein or peptide fractionation techniques (listed above).
  • Peptide fragmentation by CID, HCD and ETD.
  • Relative quantification of proteins and proteomes by stable isotope labeling (SILAC, TMT or dimethyl), using high resolution and high mass accuracy LC-MS and LC-MS/MS.
  • Identification of phosphorylation and other post-translational modifications on single protein level.
  • Data analysis for all of the services listed above.
  • For protein identification, Mascot is used as the default search engine. Databases can be customized to the user’s needs.
  • For protein quantification, we analyse data via MaxQuant, Proteome Discoverer or IsobarQuant.