If you haven't seen this paper, you should. This study presents compelling evidence of an entirely new class of molecules that we had zero idea were even around. The ramifications of this are at the level of text-book-altering. Glycosylated short RNAs sticking on the surface of cells doing -- presumably -- super important things. The initial study only identifies a few and they appear to be annotated as:
"Non coding RNA" -- which means, they don't appear to make proteins. Why are they there? No idea. Till now. (Kinda).
I just realized that picture above from the PDF cuts off 5 of the author names. Pedro, Benjamin, Alex, Benson and Karim deserve to have their names shown in the PDF. Get your act together, ElfSeverer. Fixed it.
Without running this out forever, these authors did some really innovative labeling and RNA stuff that I'm sure makes sense to RNA people. And these cool molecules disappear when you treat with something that cleaves RNA or cleaves sugars. They also did some top notch LCMS work. You can find all their RNA data on public repositories, but I can't find the LCMS files. It was obviously something that was secondary to their goals.
It is not, however, secondary to my goals. And I bet that there are a whole bunch of people weird enough to read a proteomics blog that don't know that there are great tools out there for looking at RNA data by LCMS. There are, in fact, even SEARCH ENGINES and a couple of them are in formats that you already know how to use.
A couple of things real fast, though.
1) Nucleotides don't like to ionize in positive mode. Neither do glycans. However at a certain size of a molecule you can pretty much stuff a proton on it somewhere, but the signal might not be great. If you haven't calibrated your instrument in negative mode since installation, you might be operating at a handicap.
2) Nucleotides LOVE to fragment. No joke. Check this out.
I highlighted it but it's from this amazing recent study
See what I highlighted above? You know what that means, right?!?!?
No, not popcorn time....geez.....it just rhymes....
What it means is that the tools are in the friendly, open, ultrapowerful, free...
They're from an older study by the OpenMS team where they used UV to crosslink RNA to proteins and then tryptically digested them to figure out what RNA is interacting with what proteins. Super cool workflow that I have always kept in my back pocket for conversations with people interested in RNA-protein interactions. It's hard to see in the screenshot above, but there are these extra yellow/green lines. What are those? They're nucleotide diagnostic ions!! No joke, this tool is super cool and really easy to use, and it's got amazing visualization capabilities. My only issue with it at all is that the diagnostic ion mass accuracy is a little wide and I can't figure out how to change it.
What if you just want to do some manual exploration? For example.....wait.....we did some weird shearing experiments of growing cells one time...right...?...I can't remember exactly why but we wanted stuff off the surface of cells without killing them. Still have those RAW files? Just curious if you see an MS/MS spectra with a HexNaC oxonium ion and a nucleotide fragment ion or 6?
My recommendation is to make multiple overlapping ranges that are just filtered on MS2. (See below)
See, I found a ton of cool stuff, but probably not enough for more than a fun 30 minute blog post. And this really does just look like the tip of an iceberg.