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A Galaxy of informatics resources for MS-based proteomics862.58 kB
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Journal article
A Galaxy of informatics resources for MS-based proteomics
Expert Review of Proteomics, Vol.20(11), pp.251-266
2023
Abstract
Introduction: Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization, and a better understanding of biological systems when integrated with other ‘omics data. Bioinformatic resources meeting analysis requirements of increasingly complex MS-based proteomic data, and associated multi-omic data, are critically needed. These requirements included availability of software spanning diverse types of analyses, along with scalability for large-scale, compute-intensive applications and mechanisms to ease adoption of the software.
Areas covered: The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses.
Expert opinion; The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.
Details
- Title
- A Galaxy of informatics resources for MS-based proteomics
- Authors
- Subina Mehta (Author) - University of MinnesotaMatthias Bernt (Author) - Helmholtz Centre for Environmental ResearchMatthew Chambers (Author) - Stamford HospitalMatthias Fahrner (Author) - University of FreiburgMelanie Christine Föll (Author) - German Cancer Research CenterBjoern Gruening (Author) - University of FreiburgCarlos Horro (Author) - University of BergenJames E. Johnson (Author) - University of MinnesotaValentin Loux (Author) - Saint Mary's University of MinnesotaAndrew T. Rajczewski (Author) - University of MinnesotaOliver Schilling (Author) - German Cancer Research CenterYves Vandenbrouck (Author) - CEA GrenobleOve Johan Ragnar Gustafsson (Author) - University of MelbourneW. C. Mike Thang (Author) - University of QueenslandCameron Hyde (Author) - University of the Sunshine Coast, Queensland, School of Science, Technology and EngineeringGareth Price (Author) - University of QueenslandPratik D. Jagtap (Corresponding Author) - University of MinnesotaTimothy J. Griffin (Corresponding Author) - University of Minnesota
- Publication details
- Expert Review of Proteomics, Vol.20(11), pp.251-266
- Publisher
- Taylor & Francis
- DOI
- 10.1080/14789450.2023.2265062
- ISSN
- 1744-8387
- Organisation Unit
- School of Science, Technology and Engineering; University of the Sunshine Coast, Queensland
- Language
- English
- Record Identifier
- 99971196302621
- Output Type
- Journal article
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