Group Leader

Hirofumi Nakagami, PhD
Hirofumi Nakagami, PhD
Group leader
Phone:+49 221 5062-224

Protein Mass Spectrometry Service

Protein Mass Spectrometry Service

Please visit our website on the Intranet for more details on our services.

The proteome is the entire set of proteins expressed by a cell at a certain time. The goal of proteomics (proteome analysis) is a comprehensive, quantitative description of protein expression and its changes under the influence of biological perturbations (Anderson and Anderson, Electrophoresis, 1998). Modern liquid chromatography-mass spectrometry (LC-MS)-based proteomics allow a large-scale identification and quantification of proteins from complex samples. With recent LC-MS systems, thousands of proteins can be analysed in a single LC-MS run.

The Protein Mass Spectrometry Service group performs large-scale proteomic analyses for all research groups at the MPIPZ. We provide a versatile proteomics platform for the institute including sample preparation, gel and liquid chromatography, sample digestion, mass spectrometry, and data analysis.

Our expertise includes:

  1. Analysis of single proteins (e.g., recombinant proteins)
  2. Identification and/or quantification of proteins in complex proteomes (Labelled- and label-free quantitative analysis, protein samples will be processed by in-solution digestion or FASP)
  3. Identification and/or quantification of post-translational modifications (PTM) of proteins (e.g., mapping PTM sites in purified proteins, phosphoproteomics with phosphopeptide enrichments)
  4. Protein pull-downs and interaction studies (e.g., identification of interaction partners by IP/AP-MS)

The core instruments of our facility include two LC-MS system:

  • Q Exactive Plus, hybrid quadrupole-Orbitrap (Thermo Scientific) coupled to Easy nLC1200
  • Q Exactive, hybrid quadrupole-Orbitrap (Thermo Scientific) coupled to Easy nLC1000

In addition to LC-MS systems, we are also equipped with an BN-PAGE analysis, 2D-DIGE equipment, Typhoon imager, Delta2D analysis software, and gel digestion robot.

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