Proteome Discoverer Software Support – Troubleshooting

Free upgrades require an active maintenance license. The maintenance license is tied to the “Discoverer_Annotation” license, which can be found in the Administration->Manage Licenses menu option in Proteome Discoverer. If the license is expired, this can be seen by checking the “Show Expired Licenses” checkbox at the top of the screen.

• Administration → Manage Licenses
• Active maintenance – allows for free upgrades/protein GO annotation

The Discoverer Annotation license has expired. To reactivate this license, you will need to purchase the Proteome Discoverer maintenance (OPTON-20141). On purchase of the maintenance, a sheet of paper with a license key will be shipped to you. This license key should be entered into the Administration->Manage Licenses page by clicking “Add Activation Code.”

Please create a bug report using the Tools->Create Bug Report option. Then send an e-mail to pd.support@thermofisher.com with a description of the issue and attach the bug report.

Warnings - will disappear when you “save” the WF (an older node version automatically updates itself)

Errors - you need to remove the offending node and use a modern equivalent (several new nodes in PD

• Go to Administration → Manage Licenses
• Click “Add License”
• Insert activation code: WUC2-1MNB-D2GX-1MZ4
• Click “Scan for missing features”
• Restart PD 2.2

1. When opening a .pdresults file from an older PD 2.x version
   • Program makes a copy of the original file with an extension .bak
   • It updates the file for PD 2.2 and saves it under the original name
   • Note: this updated file cannot be opened in an older PD version
2. .msf files from PD 1.4
   • We suggest reprocessing the data (from the .raw file)
   • As Consensus WF would have to be run anyway
   • Too many changes in quan data processing

A selected set of row filters can be applied when opening a Result file where no filter set had been specified in the Display Settings node of the CWF. Prepare such filter set for one of your opened results files, save it, and then deploy it under Administration → Configuration → Display Settings → Default Filter Set

A pre-defined layout can be applied when opening a Result file where no layout had been specified in the Display Settings node of the CWF. Prepare such layout for one of your opened results files, save it, and then deploy it under Administration → Configuration → Display Settings → Default Layout.

Protein Center serves as a controlled static reference. The Swiss-Prot database therein has not been updated beyond the specified date. The user should obtain FASTA databases from the original sources if he wishes to include the most recent updates.