Project title
Development and optimisation of a DIA-NN workflow for scalable proteomics
Collaborators and funding
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Precision Nutrition research group, School of Life and Environmental Sciences (CSP), University of Sydney
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Bioinformatics Group, Sydney Informatics Hub, University of Sydney
Contact(s)
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Cali Willet, Sydney Informatics Hub, University of Sydney cali.willet@sydney.edu.au
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Carsten Schmitz-Peiffer, Charles Perkins Center, University of Sydney carsten.schmitzpeiffer@sydney.edu.au
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Lewin Small, Charles Perkins Center, University of Sydney, lewin.small@sydney.edu.au
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Georgie Samaha, Sydney Informatics Hub, University of Sydney georgina.samaha@sydney.edu.au
Project description and aims
Scanning SWATH is a novel method that now enables rapid mass spectrometry of hundreds of peptide samples.DIA-NN is a popular tool for processing data-independent acquisition (DIA) proteomics experiments. However, throughput of DIA-NN is currently limited and processing large cohorts requires days of computing time and batch processing. We will develop a scalable bioinformatics workflow that optimises the execution of DIA-NN for execution on high-performance computing infrastructure and commercial cloud to meet the growing demand of high-throughput proteomics experiments
The workflow will enable rapid generation of unbiased quantitative data concerning the proteins present in high numbers of complex tissue samples, obtained for example under different dietary or genetic conditions. This will enable further mechanistic investigation of the phenotypes observed.
How is ABLeS supporting this work?
This work is supported through the software accelerator scheme provided by ABLeS. The supports includes 44 TB temporary storage and 10 KSUs per quarter.
Expected outputs enabled by participation in ABLeS
A computational workflow for DIA-NN software-based processing of scanning SWATH data. The workflow development can be followed on GitHub.
These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.