A scientist at the Chair of Proteomics and Bioanalytics working at the mass spectrometer.
A scientist at the Chair of Proteomics and Bioanalytics working at the mass spectrometer.
Image: B. Küster / TUM
  • Research news
  • Reading time: 2 MIN

A milestone for biomedical researchMass spectrometry-based draft of the mouse proteome

Proteins control and organize almost every aspect of life. The totality of all proteins in a living organism, a tissue or a cell is called the proteome. Using mass spectrometry, researchers at the Technical University of Munich (TUM) characterize the proteome, or protein complement of the genome, in important model organisms. In 2014, a team at the Chair of Proteomics and Bioanalytics reported a draft human proteome for the first time, followed by that of the model plant Arabidopsis thaliana in 2020, and now that of the most common laboratory mouse.

The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. “We present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues. These molecules are cellular regulators of normal as well as pathological processes," says Bernhard Küster, Professor of Proteomics and Bioanalytics.

The proteomes of humans, animals and plants have many similarities

The researchers now show in a Nature Methods publication what insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes and thousands of isoforms, proteins that arise from the same gene but differ in structure.

Furthermore, 50,000 phosphorylation sites could be found. These are specific and particularly important parts of proteins that regulate processes in the cell. In other words, the research work provides information about how many of the approximately 20,000 mouse genes exist as proteins, where they are expressed, in what quantities they occur and how active they are.

Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. "We leverage the mouse proteome by integrating more than 400 phenotypic drug and radiation response data sets with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for drug sensitivity and resistance," says Piero Giansanti, Ph.D., first author of the study.

Protein catalog freely available

The unique atlas complements other molecular resources for the mouse. This information is freely available in the online databases ProteomicsDB and PACiFIC.


Giansanti, P., Samaras, P., Bian, Y. et al.: Mass spectrometry-based draft of the mouse proteome. Nat Methods (2022). doi.org/10.1038/s41592-022-01526-y

More information:

This work was supported by:
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)

Technical University of Munich

Corporate Communications Center Dr. Katharina Baumeister

Contacts to this article:

Prof. Dr. Bernhard Küster
Technical University of Munich
Chair of Proteomics and Bioanalytics
TUM School of Life Sciences

Related articles at www.tum.de

Graphic of a thale cress integrated in a bar chart.

A molecular map for the plant sciences

Plants are essential for life on earth. They provide food for essentially all organisms, oxygen for breathing, and they regulate the climate of the planet. Proteins play a key role in controlling all aspects of life…

The authors Mathias Wilhelm, Tobias Schmidt and Siegfried Gessulat.

Artificial intelligence boosts proteome research

Using artificial intelligence, researchers at the Technical University of Munich (TUM) have succeeded in making the mass analysis of proteins from any organism significantly faster than before and almost error-free. This…

Mathias Wilhelm, Professor Bernhard Küster and Daniel Paul Zolg (f.l.t.r.) in discussion about the ProteomeTools Peptide Library called PROPEL. (Photo: Andreas Heddergott/ TUM)

Milestone for the analysis of human proteomes

Researchers led by the Technical University of Munich (TUM) report on the synthesis of a library of more than 330,000 reference peptides representing essentially all canonical proteins of the human proteome. It is a major…