I sat this paper to the side because I didn't know what the heck to think about it. It sounded like a funny concept -- then I skipped the nice and short (Open Access) paper and just went to the tool!
What? Who thought this would be a good idea? Why didn't anyone think of this before? Then...NO WAY...it CAN'T BE THAT FAST AND WORK!! Who can I send this paper to immediately? Wait... I might be the only person who will be this excited...just put it on the blog...
This was my brain on PGx.
If you want to go through this roller coaster of an experience...you can use the tool here.
What's it do? It takes your peptide list and then makes a new file out of it. This file is called a BED file and it is a mapping of all the peptides you found -- to their specific place in the genome.
No -- seriously this is pretty cool for the proteogenomics stuff -- because it saves you a lot of steps. Have you tried to do this with the (AWESOME!) free tools out there? It is really super hard (if you're as dumb as me). In this paper they state that it takes 140 steps to get this far using the Galaxy tools...which might be an exaggeration.....
There is a catch, however. The web interface is just a taste of the power that you have. You have to go to Python to use all the tools they show in the paper, but if you just have a couple human peptides you want to know more about -- the web interface is good enough -- and it'll make you a BED file for your entire peptide list in a few seconds! I loaded 34k PSMs which it reduced down to 21k non-redundant sites!
If you are using PD 2.1 you'll have to export your peptide or PSM list and then remove the flanking residues.
I did it with "Text to Columns" in Excel.
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