Oral Presentation AUS-oMicS 2025

Mass spectrometry and HPC: the time is now! (#50)

Johan Gustafsson 1 , Georgina Samaha 2 , Ziad Al Bkhetan 1 , Ben Crossett 3 , Rohan Lowe 4 , Chi Nam Ignatius Pang 5 , William Klare 5 , Katharine A Michie 6
  1. Australian BioCommons, https://www.biocommons.org.au/
  2. Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, New South Wales, Australia
  3. Sydney Mass Spectrometry, The University of Sydney, Sydney, New South Wales, Australia
  4. La Trobe University Proteomics and Metabolomics Platform, La Trobe University, Bundoora, Victoria, Australia
  5. Australian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales, Australia
  6. Structural Biology Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia

Mass spectrometry, and in particular its omics focused fields (e.g. proteomics), has reached the point where experimental complexity, sample numbers, and sample sizes all dictate a need to access greater compute resources beyond those immediately available within research institutions. Knowing what to access and when, however, is still non-trivial. Commercial clouds, while powerful and readily accessible, can be cost prohibitive. National high performance computing (HPC) systems are powerful and relatively inexpensive, but have not traditionally been geared for bioinformatics and therefore require the right expertise to access and leverage effectively. Additionally, understanding the impact of software licenses, which software can be deployed on which systems, and verifying if it is technically and scientifically valid to do so, remains challenging.

This presentation will outline examples of collective efforts within the Australian research community to on-board life science domains to HPC and make effective use of national computational resources to accelerate research. Included are examples from community efforts in genomics and computational structural biology, as well as the ecosystem of services, platforms, and standards that support these efforts via the Australian BioCommons and its infrastructure partners. Finally, taking these collective efforts as a blueprint, the characteristics and challenges of omics domains that employ mass spectrometry will be considered. These include, 1) identifying ways to accommodate a fragmented software landscape that ranges from open source / open access, to those with restrictive licence conditions, 2) engineering solutions for scaling tasks that are not designed for HPC, and 3) the need to contextualise complex results using approaches such as pathway analysis. We will propose potential pathways that may be needed to open up the use of peak compute systems for proteomics, metabolomics, glycomics and collaborative multiomics studies, and we hope that this will continue to stimulate community-led discussion in this area.