Proteome Discoverer 2.0 videos

Hey guys!  These aren't perfect and I'll update them as I improve them over time.  The goal is to help you get going with PD 2.0

1.       Loading a FASTA database from your hard drive:
2.       Creating a custom FASTA database:
3.       How to use the Administration menu:
4.       How to configure your Mascot server:
5.       How to set up a simple peptide ID workflow in PD 2.0:
6.       How to use the consensus steps in PD 2.0:
7.       How to process M2 TMT and iTRAQ MS2 data:
8.       How to organized a reporter quan experiment in PD 2.0 (Part I):
10.   How to organize a reporter quan experiment in PD 2.0 (Part 2, the results):
11.   How to process SILAC data:
12.   Reprocess consensus report data in PD 2.0 (new version) :
13.   How to perform label free relative protein quan in Proteome Discoverer 2.0:
14.   How to set up a complex relative label free quan experiment in PD 2.0 (multiple fractions):
15.   How to use the Annotation nodes:
16.   How to use the Proteome Discoverer 2.0 Daemon:
17.   Set up a search with multiple search engines:
18.   How to export data to search in another program:
19.   Peptide FDR discussion (PSM validation nodes):

20.   Protein Validation nodes:


21.  How to extract only proteins with a specific post-translational modification:
22.  How to process global peptide and global prosphoproteomics data together into one single report:


  1. The presenter needs to add sound and the mouse needs to go slower to demonstrate everything. It is very hard to follow the mouse and it's to fast.

  2. May I run the ABsciex (TT5600) on PD2.0 for Sequest search and DIA umpire?

    1. Sure! PD will accept whatever data you give it. You'll have to convert it to MGF or another format, but DIA umpire would ouput a format the PD would take no problem!

  3. These tools are a valuable tool for individuals new to Proteome Discoverere

  4. These are a great resource. Many thanks for taking the time to make them available!

  5. Hi there, do you have a video on how to open a file processed in PD1.4 with PD2.1? I've been watching your videos and reading the help files but not getting any where. Is it even possible, does it all have to be processed in PD2.1? Thanks

    1. Maz, I added a new post with some screenshots. Hope that helps!

    2. For future reference its this one:

  6. Hi Ben,

    Is there a way to define the study in Daemon 2.0? When I submit the files from Daemon the PD 2.0 gives the name of the study as Daemon temporary study. Is there a way to change that. Thanks