I2MS -- We're looking at RAW data the wrong way for top down!

I've had a lot of pictures on my desktop from the I2MS papers. (Paper 1, above and 2, below)

Full honesty -- I have no idea what is happening here. I might try to puzzle it out while I'm writing this.

What I do get -- when I do intact protein mass spec I need a TON of signal and nice chromatography to keep it from giving me crap like this...(from paper #2). In particular, if this is complex? You'll see junk like this all the time.

When I get garbage spectra like this I conclude 1) something big is here and 2) its going to take a lot of work to fix this so I can figure out what the hell it is -- if it's possible at all.

From this same garbage spectra, however, reprocessing this with the I2MS approach (the 2 is supposed to be superscript and I don't know how to do it) -- you can supposedly get something like this --

WHAT?!?!?

Okay -- so you don't have to take the authors' words for this -- you can just go to the supplemental (from the second study) and download the software. It's called CADMIUM. You will need to unzip it twice. And then you'll get a deceptively simple looking interface.

There are demo files in the supplemental. There are only 8 buttons here, but you're going to need to read the directions. If you just start dumping stuff in it and pushing the buttons it'll get angry.

Okay -- full disclosure -- I've been working on this post for like 2 days off and on. Trying to get something from the 2 papers to click in my head so I know what is happening.

I know enough to realize that this is important and I'm comfortable enough with myself and my place in this world to say that I still don't know what is happening. If someone wants to give me an ELI5 or a crayon drawing I'll make time for it!