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@ARTICLE{Mehta:284410,
      author       = {S. Mehta and M. Bernt and M. Chambers and M. Fahrner$^*$
                      and M. C. Föll$^*$ and B. Gruening and C. Horro and J. E.
                      Johnson and V. Loux and A. T. Rajczewski and O.
                      Schilling$^*$ and Y. Vandenbrouck and O. J. R. Gustafsson
                      and W. C. M. Thang and C. Hyde and G. Price and P. D. Jagtap
                      and T. J. Griffin},
      title        = {{A} {G}alaxy of informatics resources for {MS}-based
                      proteomics.},
      journal      = {Expert review of proteomics},
      volume       = {20},
      number       = {11},
      issn         = {1478-9450},
      address      = {Abingdon},
      publisher    = {Taylor $\&$ Francis Group},
      reportid     = {DKFZ-2023-01999},
      pages        = {251-266},
      year         = {2023},
      note         = {2023 Jul-Dec;20(11):251-266},
      abstract     = {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.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.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.},
      subtyp        = {Review Article},
      keywords     = {Bioinformatics (Other) / Computational workflows (Other) /
                      Galaxy platform (Other) / Mass-spectrometry (Other) /
                      Multi-omics (Other) / Reproducibility (Other) / proteomics
                      (Other)},
      cin          = {FR01},
      ddc          = {610},
      cid          = {I:(DE-He78)FR01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37787106},
      doi          = {10.1080/14789450.2023.2265062},
      url          = {https://inrepo02.dkfz.de/record/284410},
}