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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: MS DOSS – The next generation of hybrid algorithms for PTM enabled peptide search (FHOOE, Hagenberg, Austria)

Gene Regulation, Stem Cells and Cancer

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Dr Viktoria Dorfer , Dr Kyowon Jeong No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Barcelona Spain Bioinformatics Data Analysis Computer Science Software Engineering

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 13: (FHOOE, Hagenberg, Austria)

Title:  MS DOSS – The next generation of hybrid algorithms for PTM enabled peptide search

Objectives: Develop a hybrid open PTM search to identify peptides at constant/low search space. This algorithm shall make use of different search strategies to be able to openly search for post-translationally modified peptides in high-resolution mass spectrometry data at constant/low search space.

Methodology: Multiple search strategies (de novo, database search, library search) shall be combined to quickly filter out false peptide candidates and reduce the search space before the search. Searches shall be open to scan for (unknown) modifications. Artificial intelligence methods (e.g., intensity prediction, fragmentation pattern prediction) shall help to identify and match candidates.

Required skills:

Basic skills in bioinformatics and (computational) mass spectrometry

Good programming skills, preferably C# and python/R

Good command of English

Expected Results: A new algorithm able to identify (post-translationally modified) peptides out of high-resolution tandem mass spectra at low search time with small search space but as an open search.

Planned Secondments: 

VIB (Belgium), duration: 2 Months; when: Year 1; goal: Integration of intensity prediction into MS DOSS.

TUM (Germany), duration: 3 Months; when: Year 2; goal: Integration of fragmentation prediction into MS DOSS.

Host: EKUT (Germany), duration: 1 Month; when: Year 3; goal: Integration of spectra deconvolution into MS DOSS.

Enrolment in doctoral programs: Ph.D. in Computer Science from Johannes Kepler University Linz

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


About FH OOE:

Being one of the strongest universities of applied sciences in terms of research in the German-speaking world, the University of Applied Sciences Upper Austria (FH OOE) is a leader in its field. It offers 68 internationally recognized academic degree programmes in four faculties at four campuses: Informatics, Communication & Media (Hagenberg), Medical Engineering & Applied Social Sciences (Linz), Business & Management (Steyr), and Engineering (Wels).

FH OOE focuses on application-oriented and innovative research in 17 thematic areas with partners from business to society.

FH OOE highly prioritizes interdisciplinary research and development. The combination of different research fields of economics, technology, and social sciences results in solutions that are even closer to users’ needs and give the economy and society a decisive lead.

The Bioinformatics Research Group of the University of Applied Sciences Upper Austria focuses on analyzing biological data. Since 2012 one part of the research group is dedicated to research in computational proteomics and has been very successful in this area. Several algorithms in the context of computational mass spectrometry, such as MS Amanda, CharmeRT, or PhoStar, have been published in recent years, showing that FH OOE is perfectly suitable for hosting and training an ESR in the field of computational proteomics.

Funding Notes

The position is fully funded for 36 months by the European Commission under the H2020 Marie Curie Innovative Training Network Programme.
Marie Curie ITNs provide a highly competitive salary to the ESR, including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance.
The eligibility criteria dictated by the European Commission under the H2020 Marie Curie Innovative Training Network Programme must be fulfilled.
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1. Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., & Mechtler, K. (2014). MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra. Journal of Proteome Research, 13(8), 3679–3684.
2. Dorfer, V., Maltsev, S., Winkler, S., & Mechtler, K. (2018). CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction. Journal of Proteome Research, 17(8), 2581–2589.
3. Dorl, S., Winkler, S., Mechtler, K., & Dorfer, V. (2017). PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search. Journal of Proteome Research, 17(1), 290–295.

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