Find valuable information.

Optimize your experiments to get the best results. We’ve compiled a detailed knowledge base of the top tips and tricks to meet your analyses needs.

View the relevant questions below:

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Troubleshooting

Getting Started

How do I connect Proteome Discoverer to my Mascot server?

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

How do I perform Multi-threaded Sequest?

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.
How do I make best use of my powerful processing PC?

By default, PD 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."

Powerful Processing PC
What is a suggested PC configuration for Proteome Discoverer?

Critical features:

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

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