Pretty soon I'm going to be rambling on about all sorts of improvement in reporter ion quan due to improvements we'll be seeing in Proteome Discoverer 2.1.
In the meantime, however, here's a great new node for PD 1.4 that improved TMT quan for this software package.
How's it work? Well, it takes a bunch of things into account, including the reporter ion isotope distribution! I can't wait to give it a shot. Unfortunately, I think I've let my PD 1.4 licenses expire and I've got to get on that....
You can download this node along with installation and processing instructions from pd-nodes.org
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