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

Tobias Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart Van Puyvelde, Yasset Perez-Riverol, Eric W. Deutsch, Bernhard Kuster, Mathias Wilhelm

Research output: Contribution to journalArticlepeer-review

Abstract

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).

Original languageEnglish
Pages (from-to)3388-3394
Number of pages7
JournalJournal of Proteome Research
Volume20
Issue number6
DOIs
Publication statusPublished - 4 Jun 2021

Keywords

  • bioinformatics
  • spectrum comparison
  • universal spectrum identifier
  • USI
  • visualization
  • web tool
  • Tandem Mass Spectrometry
  • Peptides
  • Software
  • Internet

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