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Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

  • Tobias Schmidt
    Tobias Schmidt
    Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
  • Patroklos Samaras
    Patroklos Samaras
    Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany
  • Viktoria Dorfer
    Viktoria Dorfer
    Bioinformatics Research Group, University of Applied Sciences Upper Austria, 4232 Hagenberg im Mühlkreis, Austria
  • 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
  • Tobias Kockmann
    Tobias Kockmann
    Functional Genomics Center Zurich, Swiss Federal Institute of Technology in Zurich/University of Zurich, 8092 Zürich, Switzerland
  • Leon Bichmann
    Leon Bichmann
    Applied Bioinformatics, Department of Computer Science, University Tübingen, 72074 Tübingen, Germany
  • Bart van Puyvelde
    Bart van Puyvelde
    ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B9000, Ghent, Denmark
  • 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
  • Eric W. Deutsch
    Eric W. Deutsch
    Institute for Systems Biology, Seattle, Washington 98109, United States of America
  • 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
  • , and 
  • 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]
Cite this: J. Proteome Res. 2021, 20, 6, 3388–3394
Publication Date (Web):May 10, 2021
https://doi.org/10.1021/acs.jproteome.1c00096
Copyright © 2021 American Chemical Society

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    Abstract

    Abstract Image

    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).

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    Cited By

    This article is cited by 12 publications.

    1. Trenton M. Peters-Clarke, Joshua J. Coon, Nicholas M. Riley. Instrumentation at the Leading Edge of Proteomics. Analytical Chemistry 2024, 96 (20) , 7976-8010. https://doi.org/10.1021/acs.analchem.3c04497
    2. Nathan H. Zhang, Eric W. Deutsch. SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of Proteome Research 2024, 23 (4) , 1519-1530. https://doi.org/10.1021/acs.jproteome.3c00882
    3. Benjamin C. Orsburn. Time-of-Flight Fragmentation Spectra Generated by the Proteomic Analysis of Single Human Cells Do Not Exhibit Atypical Fragmentation Patterns. Journal of Proteome Research 2023, 22 (3) , 1003-1008. https://doi.org/10.1021/acs.jproteome.2c00715
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