Proteome Discoverer 2.4 1-Year Maintenance (11+ copies) - FAQs

ProteinCenter 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 they wish to include the most recent update.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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 Consensus Workflow (CWF). Prepare such a layout for one of your opened results files, save it, and then deploy it under Administration -> Configuration -> Display Settings → Default Layout.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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 Consensus Workflow (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

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

When opening a .pdresults file from an older Proteome Discoverer (PD) Software 2.x version:
- The 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

For .msf files from PD 1.4, we suggest reprocessing the data (from the .raw file):
- As Consensus Workflow (CWF) would have to be run anyway
- Too many changes in quantitative data processing

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Go to Administration -> Manage Licenses
Click “Add License”
Insert activation code: WUC2-1MNB-D2GX-1MZ4
Click “Scan for missing features”
Restart Proteome Discoverer Software 2.2
View example here.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Warnings - will disappear when you “save” the Workflow (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 Proteome Discoverer Software)
View example here.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

This means that the Discoverer Annotation license has expired. To reactivate this license, you will need to purchase the Proteome Discoverer Software maintenance (Cat. No. 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”.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Free software 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 Software. If the license has expired, this can be seen by checking the “Show Expired Licenses” checkbox at the top of the screen.
Go to Administration -> Manage Licenses
Active maintenance - allows for free upgrades/protein GO annotation
View example here.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Go to Administration -> Manage Licenses
Navigate through products to the respective Proteome Discoverer Software version
Click on “Discoverer_Base”
See the “Entitlement ID” bottom right
View example here.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Critical features include:

- SSD drive for OS as well as separate SSD data drive (2 TB recommended)
- 64 GB memory
- Intel Xeon processors

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

By default, Proteome Discoverer Software allows simultaneous processing of 1 PWF and 1 CWF. If your hardware is powerful enough, you may increase this number.

Go to Administration -> Configuration -> Server Settings. Define the new values under “Parallel Job Execution“.

View this example.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Administration -> Configuration -> Sequest

Set Workload level to:

“Automatic - True” for Sequest HT to perform as many parallel tasks as there are available cores
“Automatic - False” - then you can define the number of parallel tasks

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Navigate to Administration->Configuration->Mascot and type in the name of the Mascot server in the Mascot Server URL field. We also recommend running the Mascot Communication Tester from the Tools menu to confirm that the connection has been made.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.