Credit for this link goes to @UCDProteomics. It's awesome to be mostly done with a QC proteomics talk and then something totally new and amazing pops up in your Twitter feed!
I can not guarantee I get this. I'm also not 100% sure I'm cool with something as wildly open source as R directly interfacing with my mass spectrometer -- but ---
This might really be worth checking out -- particularly if you've got an R BionformaGician around anyway and you haven't instituted a full out QC protocol on all your stuff!
They Shiny App interface looks really super friendly and non-intimidating. The number of variable assayed may not be any more than what we're currently implementing (sProCoP/AutoQC), and I should probably do some stuff rather than digging through details I probably wouldn't understand anyway, but PNNL has a tendency to make some really good software -- maybe not the most dumb person (me) friendly software, but I bet this is worth taking a look at!
You can download QC-Art here!