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Mass spectrometry & bioanalysis

In order to answer complex biomedical questions, we must first understand the molecular composition of a system under investigation and the ways in which this system’s components interact. Both the expertise and the equipment needed to do so are to be found in the fields of peptide synthesis and high-throughput mass spectrometry.

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All of the services available are complementary in nature and comprise a wide variety of methods ranging from the targeted study of individual molecules (e.g. via molecular markers, purification, activation) to the absolute quantification of proteins or classes of metabolites.

Core Facility for High-Throughput Mass Spectrometry

Photo: Wiebke Peitz, Charité.

Proteins and metabolic products provide an insight into the effects of genetic and environmental factors and how their interaction might affect a person’s overall health. The accurate, comprehensive and quantitative analysis of these biomolecules therefore holds great potential, particularly in the areas of clinical research and precision medicine.

The facility was established and equipped to support the analysis of large series of samples, such as those used both in systems biology research and in clinical and epidemiological studies. This includes the analysis of body fluids such as blood plasma, blood serum, urine and cerebrospinal fluid.

In addition to being available to all of Charité’s research centers and research groups, the facility’s services are also available to external users and research partners.


This is a relatively new facility and will start to accept samples from 2020. All projects must be discussed in detail before access can be granted. This will ensure the optimal use of the capacities available:

  • LC-MS and LC-MS/MS analyses using DDA or DIA as the preferred method
  • Protein identification
  • Relative and absolute quantification
  • Descriptive and functional data analyses
  • Pattern recognition, classification and prediction using machine learning


The facility has access to the following:

  • Quadrupole/Orbitrap mass spectrometer
  • Linear ion trap/Orbitrap mass spectrometer
  • Triple quadrupole mass spectrometer
  • Quadrupole/time-of-flight mass spectrometer
  • Automated sample preparation
  • Bioinformatics Service


+49 30 450 528 317

Peptide synthesis

Charité’s Peptide Synthesis Facility offers a synthesis and purification service for both smaller and larger peptides.

We produce both simple and modified peptides, all of which are offered to mg scale. This includes processes such as biotinylation, acetylation and methylation. We also specialize in peptide conjugation, i.e. the coupling of peptides to KLH, BSA or other carrier molecules. We also offer fluorescent labeling and cyclic peptides.

Peptide synthesis services include:

  • Fluorescent labeling
  • Phosphorylation
  • Conjugation (coupling to carrier proteins)
  • Biotinylation/acetylation/methylation of peptides
  • Introduction of unusual amino acids
  • Cyclization

Wherever necessary, synthesized peptides will be purified and analyzed using HPLC and MALDI Mass Spectrometry.


  • Peptide synthesis equipment: Applied Biosystems 433A Peptide Synthesizer
  • MultiSynTech Syro Multiple Peptide Synthesizer
  • CEM Liberty Blue/1 Microwave Synthesizer
  • Preparative and analytical HPLC systems (Shimadzu)
  • MALDI Mass Spectrometer (Voyager DE-pro, AB SCIEX)
  • Christ freeze dryers, precision scales


+49 30 450 528 030