CF Proteomics

The facility provides a complete platform for the identification and quantification of proteins using mass spectrometry. We are equipped with state-of-the-art chromatography systems and mass spectrometers that enable multiple MS and LC-MS/MS experiments:

  • Orbitrap Fusion Lumos Tribrid mass spectrometer (high resolution ESI mass spectrometer – Thermo) coupled to nanoAcquity UPLC
  • Q-Exactive HFX mass spectrometer (high resolution ESI mass spectrometer - Thermo) coupled to MClass nanoAcquity UPLC (Waters)
  • 1260 Infinity (HPLC) equipped with fraction collector for offline fractionation by high pH reverse phase chromatography (Agilent)
  • Sample preparation robot (in-gel digestion of large sample sets)

In addition, the facility provides a wide-range of software and bioinformatics tools for data analysis and interpretation:

  • Spectronaut (Biognosys AG)
  • SpectroDive (Biognosys AG)
  • SpectroMine (Biognosys AG)
  • Mascot Server (Matrix Science)
  • Peaks Studio (Bioinformatics Inc)
  • Proteome Discoverer (Thermo)
  • MaxQuant (Freeware, Max Planck Institute, Martinsreid)
  • Scaffold (Proteome Science)
  • Isobarquant (Cellzome AG)
  • Multiple in house written procedures based on R\Bioconductor
Workflow of a typical quantitative proteomics experiment
FLI: Proteomics Workflow
  • Identification and quantification of proteins using mass spectrometry
  • Preparation of peptides from different sample types (cells, tissues, etc…)
  • Peptide labeling for protein quantification (dimethyl labeling, TMT)
  • Off-line peptide fraction by high-pH reverse phase
  • De-novo sequencing of proteins
  • Processing of protein-protein interaction samples (BioID/Apex/GFP Trap)
  • Post-translational modification enrichment and quantification (Phosphorylation/Acetylation)

Anyone wishing to perform a proteomics experiment with the facility should contact the facility well in advance of any sample preparation steps, in order that through discussion, the best experimental design is achieved for the desired outcome of your experiment. Failure to do so may result in issues handling your samples or in the worst case they cannot be measured (eg. protocols don’t exist to handle them in the way you prepared).

Internal users:
Download (pdf) Sample Request Form

External users:
Please inquire.

Team (incomplete due to Data protection)

Name Phone Email Position
Joanna Kirkpatrick --- Core Facility Manager
Karl-Heinz Gührs +49 3641 656432 Staff Scientist
Erika Kelmer Sacramento +49 3641 656200 Postdoc
Norman Rahnis +49 3641 656856 Technical Assistant
Alessandro Ori +49 3641 656808 Scientific Supervisor

* incomplete due to Data protection

For publications of individual CF members:  publications search 


Dr. Joanna Kirkpatrick

Joanna Kirkpatrick
CF Manager
+49 3641 65-6164

Alessandro Ori
Scientific Supervisor

Group Website

Overview CF Proteomics

Overview CF Proteomics
Overview CF Proteomics