Proteomics

Services

The image shows a cluster of blue circles intertwined with colorful, abstract shapes and patterns. The letter "T" appears multiple times within the composition, suggesting a scientific or educational context related to molecular structures or interactions.

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

A flowchart illustrating a proteomics workflow. It shows steps from cell extraction to protein digestion, separation, detection through mass spectrometry, and interpretation. The process involves collaboration between customers and a core facility, highlighting data analysis as a final step.

We assist you in planning your proteomics project, give advice on protein extraction methods and agree with you on the best analysis workflow for your needs.

After you have completed the extraction of the proteins in your laboratory and labeled the samples in randomized order, you can create a project in our booking system and submit the samples to us. Please note that we are only allowed to accept sample material of security level 1.

We will digest and measure the proteins using the agreed methods and then analyze the data.

We conduct a final meeting to evaluate the complete workflow of your project.

More detailed information on our protein lysate requirements and sample submission can be found in the Links section, PCF User Guide.

Please feel free to contact us.

Instrumentation

Our LC-MS systems are equipped with Orbitrap-based mass spectrometers, the Orbitrap Exploris 480 from Thermo Fisher Scientific or the Orbitrap Astral Zoom Analyzer. 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.

Technology Development

Close-up view of a laboratory instrument, showcasing a metallic chamber with a reflective surface and a precision mechanism connected to it. The scene highlights intricate parts of the device designed for scientific experimentation or analysis.

Improving protein extraction together with our customers
Spatial proteomics
Adaptation and development of various MS measurement methods
Plasmaproteomics

Team

Dr. Shiva Ahmadi
Frederic Bethke

Technician (LC-MS)
Gerhard Erben

Engineer (LC-MS)
Sabine Fiedler

Technician (Sample Preparation)
Dr. Dario Frey

Postdoctoral Researcher
Ramona Irsevic

Technician (Sample Preparation)
Denise Jansen

PhD Student
Anna Neuerburg

Technician (Sample Preparation)
Martin Schneider

Scientist (Bioinformatician)
Kai Schönberger
Dr. Piotr Zadora

Postdoctoral Researcher

Publications

2024 - Blood

T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia

Philipp M Roessner, Isabelle Seufert, Vicente Chapaprieta, Ruparoshni Jayabalan, Hannah Briesch, Ramon Massoni-Badosa, Pavle Boskovic, Julian Benckendorff, Tobias Roider, Lavinia Arseni, Mariana Coelho, Supriya Chakraborty, Alicia M Vaca, Mariela Sivina, Markus Muckenhuber, Sonia Rodriguez-Rodriguez, Alice Bonato, Sophie A Herbst, Marc Zapatka, Clare Sun, Helene Kretzmer, Thomas Naake, Peter-Martin Bruch, Felix Czernilofsky, Elisa Ten Hacken, Martin Schneider, Dominic Helm, Deyan Y Yosifov, Joseph Kauer, Alexey V Danilov, Moritz Bewarder, Kristina Heyne, Christof Schneider, Stephan Stilgenbauer, Adrian Wiestner, Jan-Philipp Mallm, Jan A Burger, Dimitar G Efremov, Peter Lichter, Sascha Dietrich, José I Martin-Subero, Karsten Rippe, Martina Seiffert

2024 - Blood

ACSL4-Associated Lipid Metabolism Is a Distinct Therapeutic Vulnerability in KMT2A-Rearranged Acute Myeloid Leukemia

Silvia Schäfer, Lola Schmitz-Hübsch, Mehak Nihal Shaikh, Silke Brilloff, Elahe Rahimian, Vida Kufrin, Sandra Küchler, Maria Fedorova, Dominic Helm, Claudia R Ball, Martin Bornhäuser, Hanno Glimm, Meritxell Alberich Jorda, Marius Bill, Alexander A Wurm

2025 - Journal of proteome research

A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities

Cristina Chiva, Roger Olivella, An Staes, Teresa Mendes Maia, Christian Panse, Karel Stejskal, Thibaut Douché, Bérangère Lombard, Andrea Schuhmann, Damarys Loew, Karl Mechtler, Mariette Matondo, Mandy Rettel, Dominic Helm, Francis Impens, Simon Devos, Anna Shevchenko, Paolo Nanni, Eduard Sabidó

2025 - EMBO reports

RAGE is a key regulator of ductular reaction-mediated fibrosis during cholestasis

Wai-Ling Macrina Lam, Gisela Gabernet, Tanja Poth, Melanie Sator-Schmitt, Morgana Barroso Oquendo, Bettina Kast, Sabrina Lohr, Aurora de Ponti, Lena Weiß, Martin Schneider, Dominic Helm, Karin Müller-Decker, Peter Schirmacher, Mathias Heikenwälder, Ursula Klingmüller, Doris Schneller, Fabian Geisler, Sven Nahnsen, Peter Angel

2024 - Cancer Research

Fungal extract screening reveals malformin C to preferentially kill glioblastoma stem-like cells via concerted induction of proteotoxic stress and autophagic flux blockade

Emma L Phillips, Sizèd van Enk, Sara Kildgaard, Silja Schlue, Mona Göttmann, Victoria Jennings, Frederic Bethke, Gabriele Müller, Christel Herold-Mende, Daniel Pastor-Flores, Martin Schneider, Dominic Helm, Thomas Ostenfeld Larsen, Violaine Goidts

2023 - Journal of Biological Chemistry

Competition for cysteine acylation by C16: 0 and C18: 0 derived lipids is a global phenomenon in the proteome

Hana Nůsková, Fabiola Garcia Cortizo, Lena Sophie Schwenker, Timo Sachsenheimer, Egor E Diakonov, Marcel Tiebe, Martin Schneider, Jasmin Lohbeck, Carissa Reid, Annette Kopp-Schneider, Dominic Helm, Britta Brügger, Aubry K Miller, Aurelio A Teleman

2024 - ACS nano

Proteomic, Metabolomic, and Fatty Acid Profiling of Small Extracellular Vesicles from Glioblastoma Stem-Like Cells and Their Role in Tumor Heterogeneity

Tolga Lokumcu, Murat Iskar, Martin Schneider, Dominic Helm, Glynis Klinke, Lisa Schlicker, Frederic Bethke, Gabriele Müller, Karsten Richter, Gernot Poschet, Emma Phillips, Violaine Goidts

2024 - NPJ Precision Oncology

A multidimensional atlas of human glioblastoma-like organoids reveals highly coordinated molecular networks and effective drugs

Changwen Wang, Meng Sun, Chunxuan Shao, Lisa Schlicker, Yue Zhuo, Yassin Harim, Tianping Peng, Weili Tian, Nadja Stöffler, Martin Schneider, Dominic Helm, Youjun Chu, Beibei Fu, Xiaoliang Jin, Jan-Philipp Mallm, Moritz Mall, Yonghe Wu, Almut Schulze, Hai-Kun Liu

2021 - Developmental Cell

A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie–Wnt signaling axis in the liver

Donato Inverso, Jingjing Shi, Ki Hong Lee, Moritz Jakab, Shani Ben-Moshe, Shubhada R Kulkarni, Martin Schneider, Guanxiong Wang, Marziyeh Komeili, Paula Argos Vélez, Maria Riedel, Carleen Spegg, Thomas Ruppert, Christine Schaeffer-Reiss, Dominic Helm, Indrabahadur Singh, Michael Boutros, Sudhakar Chintharlapalli, Mathias Heikenwalder, Shalev Itzkovitz, Hellmut G Augustin

2022 - Molecular Cancer

Comprehensive proteomic profling of serum extracellular vesicles in patients with colorectal liver metastases identifes a signature for non-invasive risk stratifcation and early-response evaluation

Kuailu Lin, Franziska Baenke, Xixi Lai, Martin Schneider, Dominic Helm, Heike Polster, Venkatesh S Rao, Nicole Ganig, Fang Cheng Wong, Lena Seifert, Adrian M Seifert, Beatrix Jahnke, Nicole Kretschmann, Tjalf Ziemssen, Fee Klupp, Thomas Schmidt, Martin Schneider, Yi Han, Tim F Weber, Verena Plodeck, Heiner Nebelung, Nathalie Schmitt, Felix Korell, Bruno C Köhler, Carina Riediger, Jürgen Weitz, Nuh N Rahbari, Christoph Kahlert

2022 - Nature communications

Direct control of lysosomal catabolic activity by mTORC1 through regulation of V-ATPase assembly

Edoardo Ratto, S Roy Chowdhury, Nora S Siefert, Martin Schneider, Marten Wittmann, Dominic Helm, Wilhelm Palm

2022 - Science

Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins

Catarina Pechincha, Sven Groessl, Robert Kalis, Melanie de Almeida, Andrea Zanotti, Marten Wittmann, Martin Schneider, Rafael P de Campos, Sarah Rieser, Marlene Brandstetter, Alexander Schleiffer, Karin Müller-Decker, Dominic Helm, Sabrina Jabs, David Haselbach, Marius K Lemberg, Johannes Zuber, Wilhelm Palm

2022 - Science Advances

Iron regulatory protein (IRP)–mediated iron homeostasis is critical for neutrophil development and differentiation in the bone marrow

Michael Bonadonna, Sandro Altamura, Elisabeth Tybl, Gael Palais, Maria Qatato, Maria Polycarpou-Schwarz, Martin Schneider, Christina Kalk, Wibke Rüdiger, Alina Ertl, Natasha Anstee, Ruzhica Bogeska, Dominic Helm, Michael D Milsom, Bruno Galy