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

  • Iso-electric focusing of proteins and peptides, using a wide range of pH gradients. Proteins can be separated as a first step in 2D gel electrophoresis. 
  • High pH (pH 10) reverse phase or SCX chromatography, for offline fraction collection, as a pre-fractionation step in peptide-based proteomics, prior to LC-MS/MS analyses.
  • SDS-PAGE gel electrophoresis on gels ranging from 7 to 24 cm. Either in 1D or 2D gel electrophoresis.
  • Various gel staining protocols: Coomassie, silver, fluorescent staining by Sypro Ruby or Flamingo, ProQ-Diamond phosphostain.
  • Laser fluorescence imaging of fluorescently stained gels.

Protein Digestion and Labeling

  • Protein digestion in-gel or in-solution, using a variety of proteases (trypsin, LysC, chymotrypsin, ArgC).
  • In-gel acid hydrolysis for determination of N- /C- termini (eg. for samples from limited proteolysis experiments).
  • Peptide purification using ZIP tips, Stage tips or OasisHLB μElution plates (Waters).
  • Phosphopeptide enrichment (using TiO2).
  • 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).
  • Identification of proteins from silver-stained gels (please see here for pre-requisites of sample preparation).
  • 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 and HCD.
  • 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.
  • Protein identification of single proteins by MALDI peptide mass fingerprinting.
  • 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 or Proteome Discoverer.
  • Reports are customised for each user to give the appropriate detail - from a coverage map in Mascot to protein summaries in Excel, to in-depth reporting of quantitative proteome analyses.

Price List (EMBL intranet only).