To overcome current limitations in published MS data accessibility, we introduce a browser-based spectrum viewer that aims to allow exploration of alternative interpretations for MS spectra and additionally: can be operated by non-specialists, is open source, can be integrated into other software, gives appropriate publication-quality output.

Spectrum Viewer is implemented totally on the client side using XHTML for menus and dialogs, SVG for spectrum and peptide display, and Javascript to drive functionality. It comprises 3 parts: (1) the core Spectrum Viewer displays peptide-spectrum matches and implements zooming, mouse-over peaks to highlight matching parts of peptide, mouse-over parts of peptide to highlight matching peaks, export SVG, and API; (2) the Auxiliary Annotator matches peptide to spectrum for given parameters and prepares the data for the Viewer; (3) these reside on a web page that provides the user control over peptides, spectra and other parameters e.g. linker mass.


  • Import peaklist
  • Specify a single peptide, a peptide pair, or a cross-linked peptide pair with linker positions
  • Modify various parameters, e.g. modifications
  • Perform annotation of spectrum based on specified parameters
  • Zoom
  • Hover on peaks to highlight sequence
  • Hover on sequence to highlight peaks
  • Export SVG
  • Successfully tested in Firefox, Chrome, Safari, Internet Explorer.

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Intended Audience

Science/Research, Developers, End Users/Desktop, Testers

User Interface


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