Petra Gutenbrunner (MPG)

About Petra

Petra Gutenbrunner is a PhD student at the Max Planck Institute of Biochemistry in Martinsried near Munich who works in the Computational Systems Biochemistry lab under the supervision of Prof. Jürgen Cox.

Before she began to study Biomedical Informatics, she worked more than six years as software engineer. During her studies, Petra held both Bachelor and Master internships at the world-renowned Wellcome Sanger Institute. There she had the privileged opportunity to acquire advanced skills in analyzing MS data. For her Bachelor’s thesis, she developed a workflow for accurate peptide identification in genomic applications. This workflow enabled refining the human genome annotation and thus novel gene identification. For her Master’s thesis, she developed a workflow to encompass all three of peptide identification, improved site-localisation of post-translational modifications and quantification in one software tool.

The identification and reconstruction of ancient proteins is challenging since they are highly modified and low abundant due to post-mortem decay. During her PhD, Petra will develop accurate tools to identify the still unknown sequences for cultural heritage material conservation, evolutionary studies, or unraveled pathways.

Read more about Petra's PhD project.


10/2014 – 09/2016 MSc in Biomedical Informatics (passed with highest distinction) at the University of Applied Sciences Upper Austria, Hagenberg Campus

10/2015 – 07/2016 Master’s thesis at Wellcome Sanger Institute, Proteomic Mass Spectrometry

Title: A Computational Proteomics Pipeline for Phosphorylation Site Localisation

10/2012 – 09/2014 BSc in Medical and Bioinformatics (passed with distinction) at the University of Applied Science Upper Austria, Hagenberg Campus

03/2014 – 08/2014 Bachelor’s thesis at Wellcome Sanger Institute, Proteomic Mass Spectrometry

Title: Comparison of Database Search Strategies for Mass Spectrometry Data Analysis

03/2014 – 08/2014 Theoretical Bachelor’s Thesis: Implementation of “Alu-Finder”:

Transposable elements are sequences in the genome that appear more frequently. Alu elements are a group of these elements and are more abundant in gene-rich regions of the genome, thus, can influence gene expression. I developed the software Alu-Finder with the aim to encompass the approaches: identification of Alu elements in a sequence, select already identified elements from a database, and calculate the similarity between sequences and is illustrated using phylogenetic trees.

10/2011 Awarded title “Ingenieurin” (“Ing.”) from Federal Ministry of Economy, Families and Youth (bmwfi)

08/2006 – 09/2013 Full-time Software engineer/Project leader Softpoint electronic GmbH & Co KG


  • Ancient Biomolecules and Evolutionary Inference

Enrico Cappellini, Ana Prohaska, Fernando Racimo, Frido Welker, Mikkel Winther Pedersen, Morten Allentoft, Peter de Barros Damgaard, Petra Gutenbrunner, Julie Dunne, Simon Hammann, Mélanie Roffet-Salque, Melissa Ilardo, J. Víctor Moreno-Mayar, Yucheng Wang, Martin Sikora, Lasse Vinner, Jürgen Cox, Richard P. Evershed, and Eske Willerslev (Annual Review of Biochemistry, in press, 2018)

  • MaxQuant goes Linux

Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann, Sule Yilmaz, Hamid Hamzeiy, Favio Salinas, and Jürgen Cox (submitted, 2018)

Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS. (J Proteome Res. 2016 Dec 2;15(12):4686-4695. Epub 2016 Nov 10.)

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. (Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.)

At: Max Planck Institute of Biochemistry

Supervisor: Jürgen Cox