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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: Multi omics data analysis in the MaxQuant and Perseus environments (MPIB, Martinsried, Germany)

Gene Regulation, Stem Cells and Cancer

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Dr Jürgen Cox , Prof Juho Hamari No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Barcelona Spain Artificial Intelligence Bioinformatics Data Science Machine Learning Networks

About the Project

PROTrEIN ( is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The network’s mission is to train a new generation of computational proteomics researchers by providing them an inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.


Subproject 5: (Host: Max-Planck-Institute of Biochemistry - MPIB, Germany)

Title: Multi omics data analysis in the MaxQuant and Perseus environments

Objectives: Development of tools and algorithms for the analysis of proteomics data in conjunction with any other omics type and their Integration into the Perseus software. These will include lipidomics, metabolomics, genomics data, as well as the integration of top-down with bottom-up proteomics data. The student will be involved in the design and implementation of new MaxQuant technology modules for metabolomics and lipidomics. Furthermore, the student contributes to the development of the MaxQB database to multi-omics integration infrastructure.

Methodology: Algorithm development in the C# based MaxQuant and Perseus environments. Database programming in the MaxQB project. Team-based programming in the Cox lab continuous integration environment.

Required Skills: Excellent programming skills. Good command of English. Background knowledge in biology or mass spectrometry is a plus

Expected Results: Several Perseus plugins applying a multitude of data integration methods. MaxQB database supporting schemas for top-down and bottom-up proteomics integration. Integration of the metabolomics and lipidomics modules of MaxQuant.

Planned Secondments:

Host: TAMPERE UNIVERSITY (Finland), Duration: 2 Months; When: Year 1; Goal: Gamification strategies.

Host: THERMO FISHER (Germany), Duration: 2 Months; When: Year 2; Goal: Algorithm development.

Host: DOMESTIC DATA STREAMERS (Spain), Duration: 1 Months; When: Year 3; Goal: Visualization strategies.

Application Procedure:

An application is solely possible via the PROTrEIN application form:

Applications must be in English. Applicants may indicate 3 ESR Projects which they would like to work on, ranking them in order to preference. Uploading reference letters is not mandatory, but applicants should be aware that referees will be automatically contacted after submission and receive a questionnaire. Candidates must provide all information before the deadline. Candidates should ensure that referees answer the questionnaire.

Application deadline: 28 February 2021


Max-Planck-Institute of Biochemistry

The Max Planck Institute of Biochemistry (MPIB) belongs to the Max Planck Society (headquarter in Munich) an independent, non-profit research organization dedicated to top-level basic research. Researchers at the MPS hold a total of far over 100 ERC grants, thereof more than 50 Advanced, 66 Starting, and 2 Synergy Grants. There are more than 80 Max Planck Institutes worldwide, 30 belong to the Biology and Medical Section. The MPIB in Munich-Martinsried is part of the local life-science-campus, where 2 Max Planck Institutes, a Helmholtz Center, the Gene-Center, several bio-medical faculties of 2 Munich universities, and several biotech-companies are close for optimal knowledge exchange.


1. Tiwary, S., Levy, R., Gutenbrunner, P., Salinas Soto, F., Palaniappan, K. K., Deming, L., Berndl, M., Brant, A., Cimermancic, P., and Cox, J. (2019) High quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis. Nat. Methods, doi:10.1038/s41592-019-0427-6.
Prianichnikov, N., Koch, H., Koch, S., Lubeck, M., Heilig, R., Brehmer, S., Fischer, R. and Cox, J. (2020) MaxQuant software for ion mobility enhanced shotgun proteomics. Mol. Cell. Proteomics 19, 1058-69, doi:10.1074/mcp.TIR119.001720
2. Sinitcyn, P., Rudolph, J.D. and Cox, J. (2018). Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data. Annual Review of Biomedical Data Science 1, 207-234.
3. Yu, S.H., Kyriakidou, P. and Cox, J. (2020) Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification. J. Proteome Res. 19, 3945-54, doi:10.1021/acs.jproteome.0c00209.
4. Yu, S.H., Ferretti, D., Schessner, J.P., Rudolph, J.D., Borner, G.H.H and Cox, J. (2020) Expanding the Perseus Software for Omics Data Analysis With Custom Plugins. Curr. Protoc. Bioinformatics 71, e105, doi:10.1002/cpbi.105.
5. Rudolph, J.D. and Cox, J. (2019) A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis. J. Proteome Res. 18, 2052–2064, doi: 10.1021/acs.jproteome.8b00927.
6. Sinitcyn, P., Tiwary, S., Rudolph, J.D., Gutenbrunner, P., Wichmann, C., Yilmaz, S., Hamzeiy, H. and Cox, J. (2018). MaxQuant goes Linux. Nature Methods 15, 401.

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