Spectra libraries contain the MS2 spectra data associated with a peptide identification. These libraries can be used for searching new MS2 data against previously generated identifications, or to compare the results of existing identifications.

LabKey Server generates and exports a redundant Bibliospec file containing spectra data from the peptides/runs you select. These files are SQLite databases, and are supported by a variety of analysis tools. Redundant libraries may contain multiple spectra for a single peptide sequence. BlibFilter can take a redundant library as input and create a non-redundant library with consensus spectra as output. Tools like Skyline expect non-redundant libraries.

Export Spectra for Multiple Runs

To export spectra data for whole runs at a time:

  • Go to the MS2 Runs web part.
  • Select the desired runs from the list.
  • Click MS2 Export.
  • On the Export Runs page, select BiblioSpec spectra library file and click Export.
  • A spectra library file is generated and downloaded to your local machine.

Export Spectra for Selected Peptides

To export spectra data from individual peptides:

  • In the Peptides (or Peptides and Proteins) web part, select the peptides of interest.
  • Select Export Selected > Bibliospec.
  • A spectra library file is generated and downloaded to your local machine.

Export Spectra for a Filtered List of Peptides

  • In the Peptides web part, filter the list of peptides to the items of interest.
  • Select Export All > Bibliospec.
  • LabKey Server will generate a spectra library from the entire list of peptides (respecting the current filters) and downloaded it to your local machine.

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