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Research Projects

Development of a complete data processing workflow for protein-protein and RNA-protein cross-linking

[call for this position closed]

Thermo Fisher Scientific

Bremen

Germany

14/15

Supervision

Bernard Delanghe
Thermo Fisher, 1st Supervisor

Mathias Wilhelm
TUM, 2nd Supervisor

Objectives

The goals are i) implementation of algorithms for classification and identification of cross-linked peptides and ii) implementation of visualization of spectra of cross-linked peptides and proteins.

Methodology

Using the existing software development kit for Proteome Discoverer the ESR will implement a complete data processing workflow for protein-protein and RNA-protein crosslinking interactions including algorithms for classification and identification of cross-linked peptides and development of algorithms for calculating FDR, PEPs, and q-values and the implementation of visualization of spectra of cross-linked peptides and proteins.

Required Skills

Programming Skills
Strong command of English

Expected results

A complete workflow for identifying and quantifying protein-protein and RNA-protein interactions within the Proteome Discoverer workflow.

Planned secondment(s)

Host: VIB (S. Degroeve), Duration: 1 Month; When: Year 2; Goal: Learn algorithms FDR calculation.

Host: TUM (M. Wilhelm), Duration: 3 Months; When: Year 2; Goal: Learn algorithms for rescoring peptide identifications.

Host: EKUT (T. Sachsenberg), Duration: 1 Month; When: Year 1; Goal: Learn algorithms for cross-linked peptides.

Enrolment in Doctoral degree(s)

Ph.D. in Bioinformatics from the Faculty of Medicine at TUM.