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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2021, 20, 6, 3388-3394
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    Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison
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    • Tobias Schmidt
      Tobias Schmidt
      Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
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      Orcidhttp://orcid.org/0000-0002-1883-6514
    • Patroklos Samaras
      Patroklos Samaras
      Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
      More by Patroklos Samaras
    • Viktoria Dorfer
      Viktoria Dorfer
      Bioinformatics Research Group, University of Applied Sciences Upper Austria, 4232 Hagenberg im Mühlkreis, Austria
      More by Viktoria Dorfer
      Orcidhttp://orcid.org/0000-0002-5332-5701
    • Christian Panse
      Christian Panse
      Functional Genomics Center Zurich, Swiss Federal Institute of Technology in Zurich/University of Zurich, 8092 Zürich, Switzerland
      SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
      More by Christian Panse
      Orcidhttp://orcid.org/0000-0003-1975-3064
    • Tobias Kockmann
      Tobias Kockmann
      Functional Genomics Center Zurich, Swiss Federal Institute of Technology in Zurich/University of Zurich, 8092 Zürich, Switzerland
      More by Tobias Kockmann
      Orcidhttp://orcid.org/0000-0002-1847-885X
    • Leon Bichmann
      Leon Bichmann
      Applied Bioinformatics, Department of Computer Science, University Tübingen, 72074 Tübingen, Germany
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    • Bart van Puyvelde
      Bart van Puyvelde
      ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B9000, Ghent, Denmark
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    • Yasset Perez-Riverol
      Yasset Perez-Riverol
      European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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      Orcidhttp://orcid.org/0000-0001-6579-6941
    • Eric W. Deutsch
      Eric W. Deutsch
      Institute for Systems Biology, Seattle, Washington 98109, United States of America
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      Orcidhttp://orcid.org/0000-0001-8732-0928
    • Bernhard Kuster
      Bernhard Kuster
      Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
      Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
      More by Bernhard Kuster
      Orcidhttp://orcid.org/0000-0002-9094-1677
    • Mathias Wilhelm*
      Mathias Wilhelm
      Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
      Computational Mass Spectrometry, Technical University of Munich, Freising 85354, Germany
      *Email: [email protected]
      More by Mathias Wilhelm
      Orcidhttp://orcid.org/0000-0002-9224-3258
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 6, 3388–3394
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    https://doi.org/10.1021/acs.jproteome.1c00096
    Published May 10, 2021
    Copyright © 2021 American Chemical Society
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    Abstract

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    Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can be either provided manually by the user (table format) or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high-quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other web sites (https://github.com/kusterlab/universal_spectrum_explorer).

    Copyright © 2021 American Chemical Society

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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 6, 3388–3394
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.1c00096
    Published May 10, 2021
    Copyright © 2021 American Chemical Society
    Request reuse permissions

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