Potential PTM depth in Astral data might be absurd...

 Like a lot of people I know, I've been downloading any Orbitrap Asstral file that has become available and been digging through it.

The MacCoss lab data is up on Panorama here. 

The files will open in QualBrowser (so...probably FreeStyle) so you can dig through them. The first thing that is extremely obvious is how unbelievably dense the data is. Sure, the TIMSTOF and ZenoTOF are absurdly fast but there is just something striking after looking at Orbi-Orbi data and then moving into Astral data in the same interface.

As I was just leisurely browsing through one file, I kept seeing a couple of my old friends like 204.086 and the smaller mass oxonium ion glycan fragments. 

I set an MS2 filter in XCalibur for 5ppm on 204.086 and -- holy cow....(example shown above is one of the gas phase chromatogram libraries.) The filter in QualBrowser for MS2 fragments has always been a pain to make and I didn't feel like making a screenshot of another file. 

I dug up Conor Jenkin's original DIDAR script that pulls out MS2 spectra that contain diagnostic fragment ions (....can't find the github link, I'll ask and put it up later -- actually, here is the script, you just need to change the text in the diagnostic ion file, I finished a GUI for it, but that paper is a bit down the pipeline) it pulled out crazy numbers of potential PTMs based on diagnostic fragment ions --

The file I ran it on (didn't scan MS2 down low enough to pick up the lys+acetyl or citrulline or lys-GG fragment ions), but these numbers are amazingly high.

It pulled out 205,000 potential oxonium ions +/- 0.002 Da of this list of fragments out of a file with like 100,000 MS2 spectra? 

Since I'm lazy and it took a long time, I didn't set it to count each one individually, so an MS2 with a very typical HCD of a single GlcNaC would produce the top 3 ions in this list and it would count that as 3. 

Still -- I run this the lazy way on files all the time to see if it is worth going in and running a PTM search and I've never pulled out 205,000 ions out of a single file. 

I know Dionex and Friends dropped like 18 preprints during ASMS and I can't read those until after I get this last June grant application out, so probably someone has looked at PTMs in Asstral data, but if not -- it looks like an absolute goldmine for unenriched PTM searches.