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.