Friday, November 23, 2018

RawTools! More than you ever even wanted to know about Orbitrap RAW data!

I've been camping off-grid in WV and missed a load of things. It seems like every single day one or three awesome new tools appears to fix a problem our field has -- or ones we haven't yet realized that we did.

RawTools runs on both sides of this.

1) I need a RawMeat Replacement
2) Wait -- this is WAY more stuff than RawMeat could do when it was alive!

First off -- you should check out the paper at JPR here.

If you can't access it cause you're back on grid, but not at work, a pre-edited print was loaded at BioRxIv a while back that is available here.

If you just want to start interrogating some darned RAW files, you can find this tool in a number of formats in a couple of places.

You can get the most recent release at GitHub here and you can get the earlier releases here.

That's a lot of links? Yup! Sure is, but check out what you can do with this awesome toolkit!

Not only can you dig into single RAW files, but you can monitor big piles of RAW files! On the left, you see the MS2 injection time increasing as the instrument displayed here got to a bunch of injections. Consequently, on E you can see that the ID rate started plummeting.

A super interesting part might be how that sensitivity of the instrument doesn't match up exactly with a subsequent drop in IDs. We've got some wiggle room on trap instruments, particularly when the fill time doesn't get as high as the transient time. I bet if we dig into this dataset (available here!) that is when the two line up (When fill time > transient).

This is just a single example of what this great new resource can do for us!

One more link, though! Once you've processed your data through this awesome package -- you can visualize it with a simple ShinyApp, either available online here or by running it locally on your computer! Pretty great, right?!?!?

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