Monday, April 13, 2015

Proteome Discoverer 2.0 is out!

PD 2.0 is now officially released!'re going to find it a little tough to use at first.

Here are some videos that will get you going.  They are rough drafts but should be a good way to help you get going.  I'll add this to the list of Pages on the Blog to the right. Where it will say "PD 2.0 Videos!"  Please be sure to watch these in HD.  P.S...more are on the way!

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:


  1. Thanks a ton Ben.. These videos would be of great help..

  2. It is time that Thermo Scientific updated their product description webpage, which currently describes version 1.1.0.