Universal Spectrum Explorer

Universal Spectrum Explorer enables comparison and visualization of peptide mass spectra across resources to support validation and analysis in proteomics.

Key Features:

• Cross-Resource Visualization: Compares peptide tandem mass spectra from different resources to support validation of experimental results across datasets and platforms.
• Data Input Flexibility: Accepts manual table-formatted spectra and retrieves spectra via the Universal Spectrum Identifier (USI).
• REST Interface: Supports real-time requests to external resources through a REST interface for automated spectrum retrieval.
• Integration with ProteomicsDB: Accesses spectra from the ProteomeTools project via integration with ProteomicsDB.
• Prosit Predictions: Produces real-time tandem mass spectrum predictions using the Prosit deep learning framework.
• Exportable Annotated Plots: Generates annotated mirror spectrum plots exportable as editable scalable vector graphics (SVG).
• IPSA Framework: Leverages the IPSA framework for spectrum comparison and analysis.

Scientific Applications:

• Spectrum Validation: Validates peptide-spectrum matches and experimental spectra by direct comparison across repositories and datasets.
• Comparative Proteomics: Compares spectra across experimental conditions or datasets to support differential analysis and reproducibility assessment.
• Prediction Benchmarking and Hypothesis Testing: Integrates ProteomeTools spectra with Prosit predictions for benchmarking prediction models and testing proteomics hypotheses.

Methodology:

Spectra are retrieved via the Universal Spectrum Identifier (USI) and REST interface, processed and compared using the IPSA framework, and can be supplemented with real-time tandem mass spectrum predictions from the Prosit deep learning framework; annotated mirror spectrum plots are exported as SVG.