PD 2.0 is now officially released!
And....you'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: 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
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