Proteomics Facility

Proteomics Facility

We provide a complete mass-spectrometry (MS) based bottom-up proteomics infrastructure for the identification and characterization of proteins as well as for the elucidation of their molecular sociology. This includes state-of-the-art nLC-MS/MS experiments employing various data acquisition strategies. We strive to serve all internal investigators by providing both access to proteomics technologies and consultancy advice for running proteomics projects.

Proteins are a key building block of all living organisms and represent the communication hub in the crosstalk between small molecules (metabolites), extra- and intracellular signals as well as the flow of genetic information (from the genome to RNAs). Hence, together with DNA modifications and non-coding RNA, proteins (and their PTMs) constitute pivotal molecular players in cellular physiology and epigenetic regulation. As a consequence, systematic protein profiling is vital to study cellular homeostasis under regular and disease conditions.

The unit offers a state-of-the-art biomolecular mass spectrometry (MS) analysis service and collaborates with internal research groups in order to develop custom-tailored protein-protein and protein-nucleic acid complex purification and MS analyses strategies to address important biological questions. Our equipment allows us to employ state-of-the-art MS/MS identification and PTM analysis of proteins, enabling the in depth characterization of proteins and protein complexes. Recently, we added targeted MS (PRM: Parallel Reaction Monitoring) as an hypothesis driven proteomics approach offering routine sub-femtomol sensitivity as well as next-generation proteomics via DIA/HRM (Data Independent Acquisition/Hyper Reaction Monitoring) to our portfolio.


In the facility, sample processing often starts with tissue/cell lysis, fractionation, digestion of the proteins with site-specific endoproteinases (like trypsin), and peptide cleanup (to remove molecules that interfere with ionization, like detergents, plasticizers, salts). The resulting purified peptide mixture is separated online by C18 reversed-phase chromatography interfaced to a mass spectrometer using nano-UHPLC systems. As the peptides elute from the column, they are ionized by electrospray ionization (ESI) and detected by MS. In the standard data-dependent acquisition (DDA) mode, masses (more precise mass-to-charge values) of intact peptides are detected by MS survey scans, which are followed by peptide fragmentation (MS/MS) to determine the sequence and post-translational modifications of the peptides (in the resulting MS/MS spectral scans).

The unit is very experienced in metabolic labelling of cells (by SILAC), which is the cornerstone for isotope-based quantitative proteomic analyses at the MS1 (survey scan) level. Quantification by isotope-labeled spike-in peptides can also be achieved. TMT labeling as an alternative isotope-based MS/MS quantification workflow, which can be highly multiplexed is currently established. Alternative quantitative approaches are label-free quantification (LFQ) that depend on the sophisticated non-linear alignment of subsequent LC-MS runs.

Selected Publications

Wang Y, Zolotarev N, Yang CY, Rambold A., Mittler G, Grosschedl R (2020)
A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin

Immunity 53(6), 1151-1167.e6

Amol Panhale, Florian M. Richter, Fidel Ramírez, Maria Shvedunova, Thomas Manke, Gerhard Mittler & Asifa Akhtar (2019)
CAPRI enables comparison of evolutionarily conserved RNA interacting regions.
Nature Communications 10, 2682.
Musa YR, Boller S, Puchalska M, Grosschedl R, Mittler G (2018)
Comprehensive Proteomic Investigation of Ebf1 Heterozygosity in Pro-B Lymphocytes Utilizing Data Independent Acquisition
Journal of Proteome Research, 17(1), 76-85.
Kebede AF, Nieborak A, Shahidian LZ, Le Gras S, Richter F, Gómez DA, Baltissen MP, Meszaros G, Magliarelli HF, Taudt A, Margueron R, Colomé-Tatché M, Ricci R, Daujat S, Vermeulen M, Mittler G, Schneider R (2017)
Histone propionylation is a mark of active chromatin
Nature Structural & Molecular Biology 24(12), 1048–1056.
Engelke R, Riede J, Hegermann J, Wuerch A, Eimer S, Dengjel J, Mittler G (2014)
The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization
Journal of Proteome Research 3(9), 3940-56.

Find more publications of Gerhard Mittler and his team on PubMed or in the MPG Publication Repository.

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