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