Proteome Discoverer 2.2 Videos!

A PD user has produced a short series of videos to help us all get going with Proteome Discoverer 2.2.

The videos don't seem to cover topics that haven't changed from PD 2.0 and PD 2.1 so I've added some links to old videos that fill in the blanks.

Setting up Proteome Discoverer 2.2 for first use:

Adding FASTA files from Hard Drive (from my PD 2.0 videos):

How to configure your Mascot Server (from my PD 2.0 videos):

What is the SpectrumRC node and how do you use it?

Getting started with label free quan with Minora!

A more in-depth look at the precursor ion quantification nodes:

Looking at the Minora results:

Finding what is significantly different in your data with Volcano plots: (updated link)

Reporter ion quantification report output:

Using Filters and setting default filters for PD 2.2:

Optimizing the MSF Files consensus node:


  1. These videos are very helpful thanks for making them available. just to let you know the volcano plots link is dead.

  2. We recently upgraded from PD 2.1 to PD 2.2 and now searches using MS Amanda fail consistently did you have any issues with this?

  3. Following link doesn't work: "Finding what is significantly different in your data with Volcano plots:"

  4. Thanks for reporting the dead link! I've updated it on both pages.

  5. Any idea why the FidoCT node available in PD 2.1 for protein validation, is not available in PD 2.2? For me that particular node was always extremely helpful.