Tackling the big metaproteomics identification challenge in hypercomplex application domains

01 October 2023 → 30 September 2026
Research Foundation - Flanders (FWO)
Research disciplines
  • Medical and health sciences
    • Structural bioinformatics and computational proteomics
    • Microbiome
metaproteomics computational proteomics proteomics bioinformatics
Project description

The field of metaproteomics, the study of the collective proteome of whole (microbial) ecosystems, has seen substantial growth over the past few years. First coined in 2004, over 35% of all papers on metaproteomics have been published after January 2020 (PubMed query on ‘metaproteom*’). Despite its rapid rise, this field still suffers from low identification rates compared to single species proteomics because of two main reasons: (1) the dense fragmentation spectra caused by co-fragmentation, and (2) the profound lack of sequence resolution in traditional search engines. In this postdoc, I will seek methodological solutions to tackle these two issues, and therefore increase the identification rate in metaproteomics. The first solution can be found in analyzing co-fragmented spectra from both DDA as well as DIA datasets. The second solution will be to further extend our state-of-the-art tool MS2Rescore, where I will combine multiple search engines, including the co-fragmentation search engines from the first solution, and will add a new predictor for ion mobility. These methodological advances will be shown on two, hypercomplex application domains: meta-immunopeptidomics and open modification metaproteomics searches.