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Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

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

Posted 09 Sep 2020
bioRxiv DOI: 10.1101/2020.09.08.287557

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 either be 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. In addition, USE can retrieve real-time prediction of tandem mass spectra from the deep learning framework Prosit. Comparison results like annotated mirror spectrum plots can be exported from USE as editable scalable high quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and seamless integration into websites (https://github.com/kusterlab/universal_spectrum_explorer).

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