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xiSPEC: web-based visualization, analysis and sharing of proteomics data.

Lars Kolbowski1,2, Colin Combe1, Juri Rappsilber1,2

  • 1Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.

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Summary
This summary is machine-generated.

xiSPEC is a new web tool for visualizing and sharing mass spectrometry data, supporting standard proteomics formats. It offers interactive views and data sharing for researchers, enhancing data analysis and collaboration.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Visualization

Background:

  • Mass spectrometry is crucial for proteomics research.
  • Standardized data formats are essential for data sharing and reproducibility.
  • Existing tools often lack comprehensive support for standardized formats and interactive visualization.

Purpose of the Study:

  • To introduce xiSPEC, a novel web-based spectrum viewer.
  • To provide a tool for visualizing, analyzing, and sharing mass spectrometry data.
  • To support standard proteomics and cross-linking experiments using standardized file formats.

Main Methods:

  • Developed a browser-based tool, xiSPEC.
  • Implemented support for mzML and mzIdentML file formats.
  • Integrated interactive visualization with annotated spectra, fragmentation keys, and quality control plots.
  • Enabled direct data upload and selection from the PRIDE repository.
  • Facilitated public and password-protected data sharing.

Main Results:

  • xiSPEC is the first browser-based tool supporting mzML and mzIdentML.
  • Offers three interconnected, interactive views of spectral data.
  • Allows users to re-annotate spectra for hypothesis testing.
  • Provides options for public or private data sharing.

Conclusions:

  • xiSPEC enhances the analysis and sharing of mass spectrometry data.
  • Its compliance with standards and interactive features improve research reproducibility and collaboration.
  • The tool is freely accessible, promoting wider adoption in the proteomics community.