Location Queensland University of Technology, Institute for Future Environments
App. deadline Applications accepted year round/until filled
  • Scholarship available
Eligibility Open to international applicants

Next generation proteomics for digital agriculture

Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH-MS) is a novel, next-generation mass spectrometry data acquisition strategy that can be universally adopted to study proteins (proteomics), lipids (lipidomics) and metabolites (metabolomics).

In comparison to traditional approaches, a major benefit of SWATH-MS is that there is no inherent bias towards the most abundant compounds during data acquisition and fragmentation data is obtained on all ionisable compounds thus effectively the technique digitally fingerprints the samples. The digital fingerprints of the samples may be exploited by re-mining them for new insights as genomic and metabolomic databases improve or as new compositional questions arise.

In order to maximise the potential of the SWATH-MS technique, generation of comprehensive and highly curated spectral libraries is critical. Furthermore, the provision of tools for analysis, dissemination and sharing of high quality spectral reference libraries will benefit the agricultural science community.

In this study, using a range of cattle, sheep and goat tissues, body fluids and cell lines banked at CSIRO, a pan-species peptide spectral repository will be generated which will serve as the foundation for future proteomics studies in ruminants using SWATH-MS technique, but that will be specifically applied to investigate the effect of heat stress in cattle in this project.

New annotation approaches including proteogenomics will be utilised to overcome the limitations of public sequence databases and to increase the utility of peptide spectral data generated.

Statistical methods for the accurate quantification of spectra at the ion, peptide and protein levels will be developed as well as tools for comparative proteomics analysis.

Details about the application process: https://www.qut.edu.au/study/phds-and-research-degrees/student-topics/next-generation-proteomics-for-digital-agriculture 

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Further Information / Application Enquiries

Dr Pawel Sadowski