Proteomics Lab: streamlining computational proteomics for life scientists
Creators: name: Gustafsson, Ove Johan Ragnar
name: Hyde, Cameron John
name: Price, Gareth Robert
name: Padula, Matthew Paul
name: Thang, Wai Cheng Mike
name: Sadowski, Pawel
name: Ward, Nigel
Publisher: name: Zenodo
Year: 2024

description: Consultations with Australian researchers have established that computational proteomics is goingthrough a major transition, where growth in experimental complexity and data set sizes, coupledwith the challenges of navigating, understanding and redeploying software from a diverse andscattered ecosystem are now significant blockers to research programs. There is thus a demonstrableneed to 1) accelerate the discovery and onboarding of proteomics researchers to both fit-for-purposesoftware and scalable computational resources, while 2) democratising the ability to access andreuse these same resources. Key to this is to also remove the need for researchers to worry aboutmanaging the underpinning research infrastructure that makes this possible.

MethodsTo address the challenges facing computational proteomics in Australia, a working group consistingof members of the Australian proteomics community, the Australian BioCommons and GalaxyAustralia has created a shared space on Galaxy Australia called Proteomics Lab(https://proteomics.usegalaxy.org.au/). This gives researchers a proteomics specific lens into thediverse capabilities accessible via Galaxy Australia, including numerous resources created by theGalaxy-P platform, curated to include tools, reference data and training of relevance to proteomics.The Proteomics Lab webpage is built into Galaxy Australia’s Media site, which uses a Pythonframework to render the webpage from a structured data schema. This simplifies the curation andupdate of content that makes up the functionality of the page.

Novel AspectThe provision of a national shared computational platform that is being tailored to the needs ofAustralian proteomics researchers.

Preliminary Data or Plenary Speaker AbstractThe Proteomics Lab (https://proteomics.usegalaxy.org.au/) provides a proteomics-centric tools list,and a central panel curated in consultation with community members. The central panel highlightscritical software (including workflows), in-built reference data, and help information (e.g. GalaxyTraining Network tutorials), all supported by an on-going collaborative effort to optimise the installedproteomics software using real world data. For example, collaboration with community researchershas allowed Galaxy maintainers to tailor MaxQuant to access more computational resources andaccommodate analysis of more typical sample set sizes (n = 120 is the current maximum possible),and in the past six months MaxQuant on Galaxy Australia has supported hundreds of jobs, submittedby researchers from 13 different Australian research institutions. In addition, users can currentlyaccess more than 90 additional proteomics software tools, supported by 32 tutorials created by theglobal Galaxy Training Network. We invite the life science research community to use ProteomicsLab, and to help us to grow the number of optimised tools, workflows and tutorials available.Collectively, we can ensure that the service continues to be fit-for-purpose and can support bestpractice implementation of proteomics in Australia.