Monday, October 10, 2016

Panorama Auto QC (SuperProCop!) -- QC your MS system on the Cloud!

I've possibly rambled about my love for SProCoP on this crazy stream-of-consciousness that is this blog. If you haven't ran across these ramblings, SProCoP is a quality control/assurance system that can be added into Skyline. You can get it here. And you can read about it here.

If you've caught any talks recently from the Skyline folks, you've probably heard about the awesome projects -- like Panorama and Chorus which are utilizing Cloud resources (which is probably gonna be super cool for most us us -- except you guys at government/military facilities that probably block this blog already...I knew China and Thermo Scientific had blocked this thing for all their employees-- but now even the U.S. Army? Come on!)...wait, was that a complete sentence?  Nope!

This new study shows that we can combine these things -- SProCoP and the processing power of the Panorama cloud into -- SuperProCop! (My name) Or... Panorama AutoQC!  This is how it works...

So...if you are one of those cutting edge targeted labs that is setting up assays in Skyline and processing/sharing results via Panorama -- BOOM!  Quality control tools at your finger tips!

Okay, so there are lots of open source tools out there that will "QC" your system. And some of them are awesome. Maybe some of them are awesome if you feel like writing a lot of source code and Python. This one? Totally awesome.

Check this thing out!

What is it? Its a chart I just generated showing 2 peptides that the Beremen lab uses at NC State uses and their relative retention times over those 2 YEARS(!!!) of runs. Look at the bottom chart, sometime around the end of January this year, the retention times of both peptides started drifting kind of high. Wonder what happened there?

Well, what if I go and plot the FWHM for the peptides picked up from each peak by flipping the Panorama AutoQC to plot the super cryptic function "FWHM"?  And then I forget how the highlighter function works in the Microsoft Snipping tool and draw a line through the peak I'm indicating and then a HUGE CIRCLE? (And I'm on vacation and way too lazy to fix it?)

You'd get this!

The first peptide got super wide at that point! The second peptide got crazy narrow. If you knew something about these peptides, then this could indicate what went wrong in your system. More importantly (!!) variations from the norm could indicate that something is wrong before you collected sub-optimal data!

1 comment:

  1. Ben,
    This question comes from your march 20, 2015 post: Where can i find # unique peptide groups in PD 2.1? If i want to determine if i'm oversampling, then you indicated #unique pep groups/# PSM's. I'm thinking #unique peptide groups from PD 2.1 is simply the # of peptide groups on the peptide group tab, and #PSM's is the # of PSM's on the PSM tab? I couldn't find # unique pep groups on the statistics tab, so i am confused.
    BTW, your blog is the BEST reference/help i have! THANKS!