Saturday, July 11, 2020

ProVision -- ShinyApp for Quick Analysis of MaxQuant Output!

"....Google Images, making weird mass spectrometry blogs even weirder, since 2009.." 

I'm running a lot of MaxQuant right now because I'm running lots of really complex samples with short BoxCar runs and -- if you to quantify BoxCar data, MaxQuant has a little box where you put a checkmark and then it does magic. There are 2 other options for processing BoxCar data.

1) Gibberish quan

(Please correct me if something has changed recently, but as long as MaxQuant works, I'm honestly cool with it for these projects)

For MaxQuant output, you have loads of options.
1) An persistently hideous spreadsheet format that Excel has even more persistently refused to open 100% successsfully for nearly a decade.
2) The ultra powerful, can do absolutely everything if you're smart enough, will do nothing whatsoever if you are not quite smart enough, constantly improving for people smart enough to run it, constantly infuriating for people not smart enough to run it the end of the day....some of us aren't getting smarter....that train has sailed....

There are other options out there that try to bridge this gap -- and here is a new web-based one (which was what I meant to type about, forgot, and then the espresso finally got to my brain, 

You can read the paper (it's open access!) or you can just hop over and try out the program online here.

Now -- it is Shiny -- so, like all R/Shiny programs it is very particular about what your rows/columns are named. There is a function in the app to rename them, but I can't get it to work. I can only proceed if I go into my proteingroups.txt and rename them there first.

What do you get from it? Fast and pretty output. (Example plots from paper shown)

There is a funny number of warnings in the online version about imputing missing values, probably an appropriate number of them, which gives you a feel for the authors thoughts on the topic.

You can also run it locally through R in case some weird blogger is uploading tons of stuff to it and it's running really really slow today. You can get it here.

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