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

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).

Automated summary

The Universal Spectrum Explorer (USE) is a web-based tool for peptide spectrum visualization and comparison. It allows users to manually provide mass spectra or automatically retrieve them from online repositories, as well as request spectra from other resources via a REST interface. The USE supports exporting annotated mirror spectrum plots as editable scalable high-quality vector graphics.