When you use the File > Export > Spectra command, you can select the spectra to export to a MGF, MZDATA, or MZML file.

For information on exporting spectra through a workflow, see Including Spectra Export in a Workflow.

Procedure

  1. Open your search results in the result file. See Organizing results.
  2. Select File > Export > Spectra.
  3. The Export Spectra dialog box opens.
  4. In the Destination Folder box, locate file where you want to save the exported spectra.
  5. In the File Type list, select the format of the file to export the spectra to:
  6. *.mgf: Mascot Generic Format (MGF) file
  7. *.mzData: MZDATA file
  8. *mzML: MZML file
  9. In the Items To Be Exported area of the Export Spectra dialog box, select the checkbox or boxes corresponding to the type of spectra that you want to export:
  10. From MS/MS Spectrum Info: Exports the spectra extracted from the spectrum file.
  11. From PSMs: Exports the spectra that identify the PSMs.
  12. From Peptide Groups: Exports the spectra that identify peptide groups. This option is available when the result file includes peptide groups.
  13. From Proteins: Exports the spectra that identify proteins. This option is available when the result file includes proteins.
  14. To export only certain spectra in the categories that you selected in the Items To Be Exported area, do the following:
  15. On the appropriate page of the result file, select the checkbox to the left of each item that you want to export.
  16. In the Items To Be Exported area of the Export Spectra dialog box, select the Checked Items Only checkbox.
  17. If you do not select the Checked Items Only checkbox, the application exports all spectra in the categories that you selected.
  18. Select Export, or to cancel this operation and any changes you made, select Close.
  19. When exporting is complete, you can open the exported file.