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The area of informatics for mass spectrometry (MS)-based proteomics data has steadily grown over the last two decades. Numerous, effective software programs now exist for various aspects of proteomic informatics. However, many researchers still have difficulties in using these software. These difficulties arise from problems with running and integrating disparate software programs, scalability issues when dealing with large data volumes, and lack of ability to share and reproduce workflows comprised of different software. The Galaxy framework for bioinformatics provides an attractive option for solving many of these current issues in proteomic informatics. Originally developed as a workbench to enable genomic data analysis, numerous researchers are now turning to Galaxy to implement software for MS-based proteomics applications. Here, we provide an introduction to Galaxy and its features, and describe how software tools are deployed, published and shared via the scalable framework. We also describe some of the existing tools in Galaxy for basic MS-based proteomics data analysis and informatics. Finally, we describe how proteomics tools in Galaxy can be combined with other existing tools for genomic and transcriptomic data analysis to enable powerful multi-omic data analysis applications.

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