Proteomics Core Facility

This facility provides a full proteomics infrastructure for the identification and characterisation of proteins.

Infrastructure in this facility is centered around state-of-the-art mass spectrometry for MS and LC-MSMS experiments. This is complemented by chromatographic and electrophoretic systems for protein and peptide separation.


The Proteomics Core Facility provides a full proteomic infrastructure for the identification and characterization of proteins. This includes various platforms for protein and peptide separation, and state-of-the-art mass spectrometry for MS and LC-MS/MS experiments.

This website intends to give guidelines for sample submission to the PCF, and to provide practical information on sample preparation.



  • Project planning, sample preparation, data acquisition and data analysis/ visualization
  • Protein identification from in-gel or in-solution
  • High resolution and high mass-accuracy MS, MS/MS, and LC-MS/MS (Q-Exactive plus, Fusion Lumos, Exploris 480) for identification and quantification of proteins in complex mixtures
  • Protein quantification by stable-isotope labeling (e.g TMT labelling)
  • Identification of post-translational modifications on purified proteins
  • Multi-dimensional peptide separation (liquid chromatography)
  • Molecular weight determination of intact proteins by ESI mass spectrometry
  • Determination of N- and C-termini of proteins and products of limited proteolysis
  • Verification of incorporation of non-natural amino acids

Techniques and approaches

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:

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
  • Peptide-Size Exclusion Chromatography for crosslinked peptides (only internal service)
Protein Digestion and Labelling
  • 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 Oasis HLB μElution plates (Waters), Sep-Pak C18 cartridges (Waters)
  • Peptide labelling with stable isotopes (TMT) for relative protein quantification
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 labelling (TMT), 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: databases can be customized to the user’s needs
  • For protein quantification, we analyse data with MS Fragger or MaxQuant

Please enquire for additional applications that may fit your needs.

About the PCF

  • More than 400 projects per year
  • Supporting research groups at all EMBL sites and external groups
  • Manages currently six mass spectrometers and eight HPLC sytems
  • Instrumentation is aimed to run 24h/7days

Services fees

ConsumablesEURO €
Desalting (per sample)20
TMT6/11-plex labelling reagent140
TMT16/18-plex labelling reagent280
High pH reverse phase offline fractionation (per sample)20
Peptide-Size exclusion chromatography (per sample)20
Measurement time
(per hour)

In order to estimate the total price for a specific type of a proteomics experiment such as, for instance, a full proteome analysis, please contact the PCF (pcf@embl.de) to discuss.


Proteomics Core Facility
EMBL Heidelberg,
Meyerhofstraße 1,
69117 Heidelberg, Germany

Tel: +49 6221 387-8167 or 387-8388
Fax: +49 6221 387-8242
Email: pcf@embl.de