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: https://vimeo.com/115595009
2.       Creating a custom FASTA database:  https://vimeo.com/115594400
3.       How to use the Administration menu:  https://vimeo.com/117010043
4.       How to configure your Mascot server:  https://vimeo.com/117042117
5.       How to set up a simple peptide ID workflow in PD 2.0:  https://vimeo.com/115592929
6.       How to use the consensus steps in PD 2.0:  https://vimeo.com/115593122
7.       How to process M2 TMT and iTRAQ MS2 data:  https://vimeo.com/117051567
8.       How to organized a reporter quan experiment in PD 2.0 (Part I): https://vimeo.com/121393236
10.   How to organize a reporter quan experiment in PD 2.0 (Part 2, the results): https://vimeo.com/121394251
11.   How to process SILAC data:  https://vimeo.com/115874330
12.   Reprocess consensus report data in PD 2.0 (new version) :  https://vimeo.com/121897580
13.   How to perform label free relative protein quan in Proteome Discoverer 2.0: https://vimeo.com/117064754
14.   How to set up a complex relative label free quan experiment in PD 2.0 (multiple fractions):  https://vimeo.com/121074081
15.   How to use the Annotation nodes:  https://vimeo.com/121397080
16.   How to use the Proteome Discoverer 2.0 Daemon:  https://vimeo.com/115875441
17.   Set up a search with multiple search engines:  https://vimeo.com/115594605
18.   How to export data to search in another program:  https://vimeo.com/63693490
19.   Peptide FDR discussion (PSM validation nodes): https://vimeo.com/64465036

20.   Protein Validation nodes:  https://vimeo.com/121399307

New!

21.  How to extract only proteins with a specific post-translational modification: https://vimeo.com/131230075
22.  How to process global peptide and global prosphoproteomics data together into one single report: https://vimeo.com/137643323

10 comments:

  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.

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

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    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!

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

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

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  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

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

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    2. For future reference its this one: http://proteomicsnews.blogspot.com/2016/10/opening-proteome-discoverer-14-results.html

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  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

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