Mass spectrometry-based proteomics offers the possibility of measuring thousands of proteins in a single run and has fundamentally changed the way that biological systems are analyzed.

To accurately and precisely quantify proteins in complex samples, we employ and further develop, in a fit for purpose manner, all commonly used approaches. These include label-free data independent acquisition (DIA) techniques and techniques encompassing different types of labels. For proteome-wide discovery, we primarily employ label-free and TMT-labeling based strategies, tailored to meet the specific needs of each study.

Schematic of an examplary workflow. A 96-well plate containing plasma samples. Arrow. Agilent Bravo pipetting robot. Arrow. Another 96-well plate containing disgested samples. Arrow. LC-MS Instrument Arrow. Spectral Data output. Arrow. QC & raw data analysis. Arrow. An Icon of a Spreadsheet.
Schematic of an examplary workflow (created with BioRender.com) © MDC | Matthias Ziehm & Philipp Mertins

Our collaborations with basic and clinical research groups encompass all areas of quantitative proteomics. This includes:

  • Profiling different biological states in cells, tissues and body fluids
  • Investigating protein interactions with other proteins, drugs and nucleic acids
  • Determining the spatial information of proteins (e.g. BioID)
  • Identifying post-translational modifications (PTMs), such as phosphorylation

Primary data analysis and interpretation are facilitated with well-established software packages, such as MaxQuant, Spectronaut, DIA-NN and also in-house developed software tools that enable protein-, post-translational modification (PTM)- and pathway-based analyses. We employ various quality control procedures such as routinely monitoring our LC-MS/MS performance with commercial standards.

Our approach ensures highly accurate and precise protein characterization of biological and clinical samples. Our proteomics services not only enhances our understanding of complex biological systems but also contributes to the discovery of disease biomarkers and therapeutic targets, paving the way for new advancements in medicine.

Service portfolio

  • Label-free proteome analysis (LFQ)
    • Data dependent (DDA)
    • Data independent (DIA)

    Label-free proteome analyses are our most commonly requested service and cover all kinds of tissues (snap frozen and FFPE), body fluids, cultured cells and pre-processed materials such as exosomes. DIA or DDA will be selected based on the specific project samples

  • Affinity purification interaction proteome analysis

    To analyze protein interaction partners for proteins, DNA/RNA or small molecules/drugs, users typically provide provide bead-based pull-down samples after capture and PBS washing. This analysis determines the interaction proteome of such pull downs. 

  • Global deep proteome profiling using TMT multiplexing

    If particularly deep global proteomes or especially post-translational modifications are sought, isobaric chemical labeling with TMT combined with high pH fractionation can be employed. In this workflow, different samples are multiplexed, enabling comprehensive quantification within each multiplexing set.

  • Global Post-translational modification (PTM) analysis

    The vast majority of proteins are post-translationally modified. Profiling a post-translational modification (e.g. phosphorylation, ubiquitination, lysine-acetylation) globally is always done in combination with a global proteome analysis, either label-free or TMT labeled deep proteome. Both the global and PTM analysis must be chosen. The ease of detecting different modifications varies, with phosphorylation - an essential signaling determinant - being the most commonly studied.

  • Additional and custom analysis services
    • Drug target identification by mass spectrometry analysis of pull-downs with bead-coupled drugs or thermal proteome profiling (PISA method)
    • Analysis of stable-isotope labeled (SILAC) samples
    • Fast scanning and ultra-sensitive mass spectrometry on Thermo Orbitrap Astral or Bruker timsTOF instruments via our collaboration with MDC
    • Targeted LC-MS/MS assays for follow-up target verification in PRM mode
    • MHC peptidome analysis
  • Scientific data analyses in collaborative projects

    In collaborative projects our experts will use diverse statistical tools and data analyses to determine significant differences between groups, correlations with numeric characteristics, clustering, enrichments.

  • Within our mass spectrometry services we employ the following as appropriate
    • Automated sample preparation using Agilent Bravo robotics
    • High pH reversed-phase (RP) peptide pre-fractionation (offline separation)
    • High resolution mass spectrometry on Orbitrap instruments, such as Thermo Orbitrap Exploris 480 coupled with liquid chromatography systems, such as Vanquish Neo
    • Raw Data processing on high performance Dell PowerEdge servers
    • Data quality control procedures such as routinely monitoring LC-MS/MS performance
    • Statistical data analysis e.g. in Perseus and R
      incl. significance testing for differences, correlations, clustering, and outlier analysis
    • Pathway- and signature-based analysis using single sample GSEA and PTM-SEA
    • User empowerment with Shiny user interfaces (collaboration with BIH core unit bioinformatics CUBI)
  • Data management and Storage

    All raw data are stored for at least 10 years on secure file servers of the BIH and/or MDC.

We are happy to discuss individual needs and look forward to working with you and supporting your research! Please see our getting started with proteomics section.

Equipment

  • Orbitrap Exploris 480 Mass Spectrometer (Thermo Fisher Scientific)
  • Q Exactive HF-X Orbitrap Mass Spectrometer (Thermo Fisher Scientific)
  • Q Exactive Plus Orbitrap Mass Spectrometer (Thermo Fisher Scientific)
  • Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Fisher Scientific)
  • nanoHPLC, EASY-nLC 1200 (Thermo Fisher Scientific)
  • UHPLC, Vanquish Neo (Thermo Fisher Scientific)
  • 96-channel sample processing robot: Agilent Bravo AssayMap
  • Offline UHPLCs: Agilent Infinity II 1260 and 1290
  • Covaris CryoPrep for tissue cryofracturing 
     

In scientific collaboration with the Max Delbrück Center for Molecular Medicine (MDC) also the following instruments might be accessible for collaborative projects:

  • Thermo Orbitrap Astral
  • Bruker timsTOF HT with PaSER module
  • Bruker timsTOF Ultra 2 (“single cell proteomics”) with PaSER module
  • Evosep One HPLC system
  • Covaris LE220Rsc focused-ultrasonicator

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