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Proteomics Platform – Core Facility

The Proteomics Platform – Core Facility (ProtCF) has emerged in 2020 from a joint initiative of the Institute of Surgical Pathology and the Institute of Molecular Medicine at the Medical Faculty of the University of Freiburg. ProtCF is headed by Prof. Dr. O. Schilling; Heisenberg Professor for Translational Proteomics at the Institute of Surgical Pathology.

The ProtCF is happy to support projects from the Faculty of Medicine, projects from other faculties of the University of Freiburg, and external projects. The goal of ProtCF is to make state-of-the-art proteomic techniques accessible to everyone. Thus ProtCF is not only measuring your MS samples and provides the instrumentation. We also give advice for experimental design, take over the sample preparation and analyze the data including statistics and data interpretation depending on your needs.

News: The Proteomics CF is happy to support a COST Proteocure" training school on proteomics.

Date: Sep 16, noon - Sep 20th noon 2024

Please contact us, if you have any questions!

Proteomics Platform - Core Facility (ProtCF): pat.proteomics@uniklinik-freiburg.de

Please find a list of common requested services below. The portfolio of the ProtCF is not restricted to this range of services. Additional services can be provided upon request!

  • Explorative quantitative proteomics / Global quantification of (sub)proteomes using Data independent acquisition (DIA) or Data dependent acquisition (DDA).
  • Identification of interaction partners / Co-immunoprecipitation (Co-IP) analysis using label-free or stable isotope labeling approaches (e.g. SILAC)
  • Quantitative proteome comparisons using labelfree and label-based techniques (e.g. TMT).
  • Identification and site-localization of selected post-translational modifications.
  • Identification of protease cleavage sites using N-terminomic techniques (e.g. PICS, TAILS).
  • Identification of gel-separated and Coomassie-stained proteins.
  • Identification and quantification of specific proteins in complex samples using targeted proteomics.
  • Proteomic Analysis of a wide variety of sample types including cells from tissue culture, tissue from animal models, patient material (fresh tissue, urine, blood serum, liquor), cryo-conserved tissue, formalin-fixed-paraffin embedded tissue, and more.
  • Data analysis for all of the services listed above.
  • Storage of raw and processed MS data in publicly available repositories for publication as requested by most peer-reviewed journals.

... and many more!

ProtCF has access to the following instrumentation:

timsTOF fleX (Bruker), coupled to an Evosep One liquid chromatography system

Q-Exactive+ mass spectrometer (Thermo), coupled to Nanoflow-HPLC

ProtCF is registered at the “Portal für Forschungsinfrastrukturen der DFG (RIsources)“.

For all publications, which include data generated by the Proteomics Platform, it is kindly requested that you acknowledge our support. More information can be found in the ProtCF – Terms of use.


Professor Oliver Schilling
Head of Proteomics Facility

Telefon +49 761 270 80610
Telefax +49 761 270 81970

Dr. rer. nat. Stefan Tholen

Telefon +49 761 270 80190
Telefax +49 761-270 81970

Lina Goncharenko (B. Sc.)

Telefon +49 761 270 80920
Telefax +49 761-270 81970



  • Patients and mice with deficiency in the SNARE protein SYNTAXIN-11 have a secondary B cell defect. Kögl T, Chang HF, Staniek J, Chiang SCC, Thoulass G, Lao J, Weißert K, Dettmer-Monaco V, Geiger K, Manna PT, Beziat V, Momenilandi M, Tu SM, Keppler SJ, Pattu V, Wolf P, Kupferschmid L, Tholen S, Covill LE, Ebert K, Straub T, Groß M, Gather R, Engel H, Salzer U, Schell C, Maier S, Lehmberg K, Cornu TI, Pircher H, Shahrooei M, Parvaneh N, Elling R, Rizzi M, Bryceson YT, Ehl S, Aichele P, Ammann S. J Exp Med. 2024 Jul 1;221(7):e20221122. doi: 10.1084/jem.20221122. Epub 2024 May 9.

  • Development of combination therapies with BTK inhibitors and dasatinib to treat CNS-infiltrating E2A-PBX1+/preBCR+ ALL Gentile G, Poggio T, Catalano A, Voutilainen M, Lahnalampi M, Andrade-Martinez M, Ma T, Sankowski R, Goncharenko L, Tholen S, Han K, Morgens DW, Prinz M, Lübbert M, Engel S, Hartmann TN, Cario G, Schrappe M, Lenk L, Stanulla M, Duyster J, Bronsert P, Bassik M, Cleary ML, Schilling O, Heinäniemi M, Duque-Afonso J. Blood Adv. 2024 Apr 10:bloodadvances.2023011582. doi: 10.1182/bloodadvances.2023011582

  • Enrichment, Characterization, and Proteomic Profiling of Small Extracellular Vesicles Derived from Human Limbal Mesenchymal Stromal Cells and Melanocytes Kistenmacher S, Schwämmle M, Martin G, Ulrich E, Tholen S, Schilling O, Gießl A, Schlötzer-Schrehardt U, Bucher F, Schlunck G, Nazarenko I, Reinhard T, Polisetti N. Cells. 2024 Apr 4;13(7):623. doi: 10.3390/cells13070623


  • Tpr Misregulation in Hippocampal Neural Stem Cells in Mouse Models of Alzheimer's Disease
    Malik SC, Lin JD, Ziegler-Waldkirch S, Tholen S, Deshpande SS, Schwabenland M, Schilling O, Vlachos A, Meyer-Luehmann M, Schachtrup C. Cells. 2023 Dec 1;12(23):2757. doi: 10.3390/cells12232757.

  • ROP39 is an Irgb10-specific parasite effector that modulates acute Toxoplasma gondii virulence.
    Singh S, Murillo-León M, Endres NS, Arenas Soto AF, Gómez-Marín JE, Melbert F, Kanneganti TD, Yamamoto M, Campos C, Howard JC, Taylor GA, Steinfeldt T.
    PLoS Pathog. 2023 Jan 5;19(1):e1011003. doi: 10.1371/journal.ppat.1011003. eCollection 2023 Jan.


  • ZBTB18 inhibits SREBP-dependent lipid synthesis by halting CTBPs and LSD1 activity in glioblastoma.
    Ferrarese R, Izzo A, Andrieux G, Lagies S, Bartmuss JP, Masilamani AP, Wasilenko A, Osti D, Faletti S, Schulzki R, Yuan S, Kling E, Ribecco V, Heiland DH, Tholen S, Prinz M, Pelicci G, Kammerer B, Boerries M, Carro MS.
    Life Sci Alliance. 2022 Nov 22;6(1):e202201400. doi: 10.26508/lsa.202201400. Print 2023 Jan.

  • Isolation of intact and active FoF1 ATP synthase using a FLAG-tagged subunit from the cyanobacterium Synechocystis sp. PCC 6803.
    Song K, Tholen S, Baumgartner D, Schilling O, Hess WR.
    STAR Protoc. 2022 Aug 16;3(3):101623. doi: 10.1016/j.xpro.2022.101623. eCollection 2022 Sep 16.


  • Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease.
    Erny D, Dokalis N, Mezö C, Castoldi A, Mossad O, Staszewski O, Frosch M, Villa M, Fuchs V, Mayer A, Neuber J, Sosat J, Tholen S, Schilling O, Vlachos A, Blank T, Gomez de Agüero M, Macpherson AJ, Pearce EJ, Prinz M.
    Cell Metab. 2021 Nov 2;33(11):2260-2276.e7. doi: 10.1016/j.cmet.2021.10.010.

  • Lipidomic and Proteomic Alterations Induced by Even and Odd Medium-Chain Fatty Acids on Fibroblasts of Long-Chain Fatty Acid Oxidation Disorders.
    Alatibi KI, Tholen S, Wehbe Z, Hagenbuchner J, Karall D, Ausserlechner MJ, Schilling O, Grünert SC, Vockley J, Tucci S.
    Int J Mol Sci. 2021 Sep 29;22(19):10556. doi: 10.3390/ijms221910556.