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

By 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

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][1]). ### Competing Interest Statement We are also thankful for EuBIC-MS for organizing the EuBIC-MS developer meeting 2020. Our tool is heavily influenced by the keynote talks and the initial prototype was developed within the hackathon. The authors wish to also thank all members of the Kuster laboratory. This work was in part funded by the German Federal Ministry of Education and Research (BMBF; grant No 031L0008A and 031L0168) and the European Union's Horizon 2020 Program under Grant Agreement 823839 (H2020‐INFRAIA‐2018‐1; EPIC-XS). The IBM infrastructure hosting ProteomicsDB and Prosit is operated and maintained by the SAP University Competence Center (UCC) of the Technical University Munich. B.K. and M.W. are founders and shareholders of OmicScouts GmbH (Freising, Germany), which operates in the field of proteomics. They have no operational role in the company. T.S., B.K. and M.W. are founders and shareholders of MSAID GmbH (Freising, Germany), which operates in the field of proteomics. T.S., B.K. and M.W. have no operational role in the company. * API : Application Programming Interface CE : Collision Energy DDA : Data-dependent Acquisition DIA : Data-independent acquisition EuBIC : European Bioinformatics Community FDR : False Discovery Rate HCD : Higher-energy Collision Dissociation HLA : Human Leukocyte Antigen HRAM : High-Resolution and Accurate Mass IPSA : Interactive Peptide Spectral Annotator MS : Mass Spectrum MSMS : Tandem Mass Spectra NPM : Node Package Manager PCC : Pearson’s Correlation Coefficient PRM : Parallel Reaction Monitoring PSM : Peptide Spectrum Match PTM : Post-Translational Modification REST : Representational State Transfer SA : Spectral Angle USE : Universal Spectrum Explorer USI : Universal Spectrum Identifier [1]: https://github.com/kusterlab/universal_spectrum_explorer

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