Bilateral NSF/BIO-BBSRC: Bayesian Quantitative Proteomics
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Integrative Biology
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Planned Impact
As well as the academic beneficiaries, the proposed research has significant prospective impact for the mass spectrometry industry and associated proteomics vendors. The proposed Bayesian Quantiative Proteomics platform will increase the amount of usable data extracted from LC-MS and therefore correspondingly increase users' return on investment. This will make commercial mass spectrometry instrumentation, which requires considerable capital and running costs, more attractive. In particular, we hope this extra research capacity will attract a wider uptake of mass spectrometry in environmental, biological and health research in industry and academia, as well as a wider audience of users and uses amongst systems biology researchers.
There is potential for direct impact through the licensing of some or all of our software tools developed, as we are working towards for other packages with Waters Inc.
There is considerable potential in this application for providing indirect benefits to UK public health, quality of life and environmental sustainability. Our aim is to establish a powerful platform for differential proteoform analysis and discovery enabling a wealth of new investigations in the biological sciences and translational medicine. Due to its success and further substantial promise, the BBSRC, UK research councils and industry have invested greatly in the systems biology approach. The potential improvements yielded by our workflow will therefore have a clear dissemination route to the public through reduced resources, costs and overheads required for discoveries realised with systems approaches in environmental, biological and biomedical science, and the characterisation of those discoveries.
The PDRAs employed on this grant benefit significantly from exposure to the wealth of proteome informatics expertise we will bring together, particularly since the PDRAs will be encouraged to play a significant role in public dissemination. All staff will benefit through being engaged within an international, cutting edge interdisciplinary project.
There is potential for direct impact through the licensing of some or all of our software tools developed, as we are working towards for other packages with Waters Inc.
There is considerable potential in this application for providing indirect benefits to UK public health, quality of life and environmental sustainability. Our aim is to establish a powerful platform for differential proteoform analysis and discovery enabling a wealth of new investigations in the biological sciences and translational medicine. Due to its success and further substantial promise, the BBSRC, UK research councils and industry have invested greatly in the systems biology approach. The potential improvements yielded by our workflow will therefore have a clear dissemination route to the public through reduced resources, costs and overheads required for discoveries realised with systems approaches in environmental, biological and biomedical science, and the characterisation of those discoveries.
The PDRAs employed on this grant benefit significantly from exposure to the wealth of proteome informatics expertise we will bring together, particularly since the PDRAs will be encouraged to play a significant role in public dissemination. All staff will benefit through being engaged within an international, cutting edge interdisciplinary project.
Organisations
People |
ORCID iD |
Andrew Jones (Principal Investigator) | |
Robert Beynon (Co-Investigator) |
Publications
Ferries S
(2017)
Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer
in Journal of Proteome Research
Collins A
(2018)
phpMs: A PHP-Based Mass Spectrometry Utilities Library.
in Journal of proteome research
Jones AR
(2020)
Proteome Bioinformatics Methods for Studying Histidine Phosphorylation.
in Methods in molecular biology (Clifton, N.J.)
Hardman G
(2019)
Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation.
in The EMBO journal
Description | We are working on statistical approaches for proteomics, and developing new software for quantification. We have now understood better how to estimate false localisation rate on phospho-peptides, and determination of differential expression by Bayesian methods. The grant is still running but grants describing these developments are in preparation / under submission. The improved understanding of signal processing has also indirectly led to the development of our lcmsWorld software for high-performance 3D visualisation of LC-MS data. |
Exploitation Route | Software is being considered for commercialisation e.g. via Follow On funding. |
Sectors | Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology |
Description | There is commercial interest from some MS vendors to take methods forward, and potentially commercialise. More to follow as this develops. |
First Year Of Impact | 2019 |