Got Proteome Discoverer 2.0?
Want to get a free upgrade that gives you awesome levels of label free proteomics capabilities?
I mentioned this before, but I just installed the nodes that are listed here on a fresh install of PD 2.0 and ran it and I'm blown away. These are really really super nice!
My recommendations (cause I don't know what I did wrong before):
1) Read the instructions
2) Download the nodes AND the processing and consensus workflows
3) Don't use a small file to test. Percolator needs to run for this to work. In PD 2.0 if you have less than 200 peptides going into Percolator it just turns off. Then the nodes can't work.
4) Revel in your new capabilities!!!!
(Look at this!!! I can find stuff in my runs that were not identified, but that were differentially (sp?) regulated in my two samples!!!! MAGIC!)
5) Remember that this is a free second party software. There is a nice mailing group you can sign up to for advice and news about the nodes. Your instrument vendor probably can't help you with these.
6) Do awesome label free proteomics!!!
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