You can export the PSMs in the results of searches performed by all supported search engines in an XML file in PepXML format. This format is an open data format developed by SPC/Institute for Systems Biology (ISB) for storing, exchanging, and processing peptide sequence assignments from MS/MS scans. It is a common output data format used by many different MS/MS search engines and subsequent peptide analyses.

The Proteome Discoverer application supports the export of search results in PepXML format version 1.17.

Procedure

  1. Open your search results in the result file. See Organizing results.
  2. Select File > Export > To PepXML.
  3. The Export to PepXML dialog box opens.
  4. Export to PepXML dialog box
    Export to PepXML dialog box
  5. In the Destination Folder box, enter the path and name of the file where you want to save the exported PSMs, or locate and select the file.
  6. Select Save in the Save As dialog box.
  7. To export only certain PSMs, do the following:
  8. In the PSMs page of the result file, select the checkbox to the left of each PSM that you want to export. For information, see Check items on the pages of a result file.
  9. In the Export to PepXML dialog box, select the Checked PSMs Only checkbox.
  10. If you do not select the Checked PSMs Only checkbox, the application exports all PSMs.
  11. Select Export, or to cancel this operation and any changes you made, select Close.