Sunday, March 15, 2015

PepShell -- New software that clues you in to conformational data

We're in that in-between stage right now, I think.  That stage where we're about to conquer bottom up proteomics.  We're maybe one or two instrument upgrades from being able to quickly and reliably get all the theoretical identifiable peptides in a cell.  The next stage (IMHO) is top down.  But this isn't a little step, its an exponential one.  To move from the goal of 1e5 peptides to 1e6 intact proteoforms....thats gonna be a while....

But we need to know more about how the protein works.  How they are interacting and how super important things that we've been ignoring, like 2D and 3D and 4D (quaternary?) peptide/protein structure is affecting things.  Biologically, the peptide sequence isn't all that important in relation to those other things.

In an effort to bridge this gap, a great team of researchers at different Belgish (is that right?) institutions, including some people from :

(an organization responsible for some incredibly useful Open Source tools for us.  you guys rock!) has launched a new piece of software called PepShell.

It is detailed in this JPR ASAP paper by Elien Vandermarliere et. al., (sorry, not open access).  The goal of PepShell is to allow us to consider the peptides identified by MS/MS in a more realistic sense -- that is, from the biologically relevant protein level.  For global proteomics, this goal is so lofty that I can't imagine applying it, though maybe you can.  The applications I imagine are for when you've narrowed down the field some.  My first run would be to dig through some pull down data I've got around here somewhere to see what PepShell makes of it.  I think this could be invaluable for protein-protein interaction studies, particularly when your lists of linear peptide data just didn't answer your questions!


  1. What hardware platform do you recommend for PD 2.0? I'm having to update a PD 1.4 computer - and won't be upgrading to 2.0 for awhile. Haven't seen the specs posted.

    1. I haven't seen the official specs yet, but I know that OmicsPCs has been working with beta copies of PD 2.0 to make sure they have an optimal product for launch. I have their old model, 8 cores with 16gb of RAM and it does quite well. The owner messaged me recently through SharedProteomics and said the new PCs blow mine away. I'd check out his site. Even if you don't buy his products his website will give you a good starting point.