Friday, May 12, 2017

MsStatsQC -- Longitudinal monitoring of targeted proteomic experiments!

Yeah! More quality control! This one is different than what I'm normally rambling about. Check this out!

Not very's still in press...may need to do something about this.... You can check it out here if you're in a hurry (and if you are doing targeted quan, you should be, this is AWESOME.)

MSStatsQC -- as you might get from the paper title -- is a method for determining your targeted peptide quan system performance over time. It looks seriously powerful and meets some standards set out by the United States Pharmacopeia (I walk by this all the time and have never been inside! Feel like I should go in after seeing they are also QC nerds!). The USP has data quality broken into these 4 components

1) Analytical instrument qualification
2) Analytical method validation
3) System suitability testing
4) Quality control checks

MSStatsQC is a freely available software package meant to address these USP requirements -- and does so with advanced statistics and graphical models. It takes a minute or two to figure out what the plots are, but once you figure out what you're looking at -- POW! -- instant information on how your instrument has been doing!

To be perfectly honest, as soon as the experimental section of the paper starts -- I have to stop. Wow, this paper is ridiculously math heavy. I'd blame it on 6am on a Friday...but I'd be lying. I don't have the background to follow whatever they're talking about. Fortunately -- I don't have to! I can just download MSStatsQC here. (

Even better, however, is the fact that they've set up a Shiny interface page so you can just run your data through their website! 

Before you put some time into it -- does it work? Albert Heck yeah it does! These authors download a ton of CPTAC 9.1 (the SRM stuff) data and show that they can automatically monitor the data as well as other studies have using software that require manual validation as the final step in QC process! We may never get to the point where manual QC validation is unnecessary, but if software can help us to do less of it and more analyzing the cool stuff it is a win for everybody!

Percolator has done this for global discovery proteomics -- is it perfect? Nope, but even the most stringent labs I know (including groups that manually checked every PSM before submitting a study) have enough data now that they only randomly monitor the quality of their peptide IDs that pass Percolator FDR (or monitor small batches of low metric ones).  MSStatsQC is a step in this direction for SRM labs. Less manually monitoring of your controls and QC metrics because it can look at tons of them at once -- through all of your data!

Are you running SRMs in your lab? You owe it to yourself to check out this software! One more thing -- you don't have to use their Shiny interface. You can download the software and integrate it into your own processing pipeline. That's how cool these authors are -- they just want you to have a better way of having higher confidence in the data you are producing -- any way you want to do it! As good as this is, I expect to see common targeted quan software directly integrating at least components of this so the rest of us don't even have to think about it.

And I found a fix for the lack of color in this post!

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