Core Facility

Proteomics

Dr. Dominic Helm

Head of Facility

The Proteomics Core Facility at the DKFZ offers services related to protein analysis for internal groups and their cooperation partners. From the digestion of the proteins to the measurement on our LC-MS instruments to the data analysis, we find out how the proteome of your samples is composed.

Services

Tryptic digestion of reduced proteins on magnetic beads.

We offer the following sample preparation services:

  • Protocols for extraction buffers and preparation of ready-to-use buffers
  • Provision of various devices for protein extraction (see Instrumentation)
  • Bead-based protein digestion (SP3)
  • SDS-PAGE, Coomassie staining and in-gel digestion
  • Peptide purifications

 

Source SP3: Hughes, Christopher S., et al. "Single-pot, solid-phase-enhanced sample preparation for proteomics experiments." Nature protocols 14.1 (2019): 68-85.

Source In-gel digestion: Shevchenko, Andrej, et al. "In-gel digestion for mass spectrometric characterization of proteins and proteomes." Nature protocols 1.6 (2006): 2856-2860.

Our workflow

Instrumentation

Our LC-MS systems are equipped with Orbitrap-based mass spectrometers, the Orbitrap Exploris 480 from Thermo Fisher Scientific. These instruments are characterized by high sensitivity and scanning speed in combination with mass accuracy in the ppm range and high resolution and are therefore perfectly suited for high-throughput proteome analysis with optimal data quality.

We are eagerly awaiting the arrival of our new Orbitrap Astral mass spectrometers in 2025.

Technology Development

  • Testing chemical enrichment methods for other relevant PTMs
  • Improving protein extraction together with our customers
  • Spatial proteomics
  • Adaptation and development of various MS measurement methods

Team

  • Employee image

    Dr. Dominic Helm

    Head of Facility

  • Employee image

    Frederic Bethke

    Technician (LC-MS)

  • Employee image

    Hannah Braun

    Intern

  • Employee image

    Gerhard Erben

    Engineer (LC-MS)

  • Employee image

    Sabine Fiedler

    Technician (Sample Preparation)

  • Employee image

    Ramona Irsevic

    Technician (Sample Preparation)

  • Employee image

    Denise Jansen

    PhD Student

  • Employee image

    Anna Neuerburg

    Technician (Sample Preparation)

  • Employee image

    Naoki Sanzenbacher

    Trainee

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    Martin Schneider

    Scientist (Bioinformatician)

Publications

2024 - Blood
2024 - Blood
2025 - Journal of proteome research
2025 - EMBO reports
2024 - Cancer Research
2023 - Journal of Biological Chemistry
2024 - ACS nano
2024 - NPJ Precision Oncology
2021 - Developmental Cell
2022 - Molecular Cancer
2022 - Nature communications
2022 - Science
2022 - Science Advances

Get in touch with us

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Proteomics
Core Facility
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Dr. Dominic Helm
Head of Facility
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