Okay...so...I'm honestly just floored by how ridiculously accurate these Prosit spectra are... Everyone should be using this tool. (Click should expand it.)
First off -- This tool doesn't require you to be a master bioinformagician or anything to use it.
Here is my simple walkthrough on how I generate Prosit spectral libraries.
At the top is a mirror plot generated in Proteome Discoverer 2.4. The top is the experimental peptide from a COVID-19 / SARS-CoV-2 preprint that came out on Monday 3/23/20. The bottom is the prediction made by Prosit on 1/27/20.
Worth noting: In earlier versions of Proteome Discoverer the MSPepSearch may not accept the Prosit spectral libraries (whateveryoucalledit.MSP). I pretty much jumped from 2.2 to 2.4 since I was doing mostly small molecule stuff for a year. If you are on an earlier version of PD 2.2, there is a solution -- MSAna (which is compatible with PD 2.1-2.4 -- all versions -- including the free versions)
You can get MSAna and the installation instructions from www.pd-nodes.org -- now you can use spectral libraries. MSAna also has several options for decoy library generation. It is worth checking out on it's own.
Back to the library vs theoretical, though!
This is the Prosit predicted fragmentation pattern for this peptide. This is a screenshot from the ridiculously handy and free tool PDV (Proteomics Data Viewer) that I use basically every day now for one reason or another.
Yo, where did y14 and y15 go? And it is kind of a neat characteristic that it only predicts that you'll see a central series of b -ions...
An experimental PSM says...?
....pretty darned close!
Okay -- that's not bad, right? However, you should go back to the top and look at the relative intensities of these fragments.....because Prosit predicts those too! Actually, here is a zoomed in clip!
A deep learning tool predicted the bottom....and the top is the real spectra from a peptide that had never been experimentally observed in unlabeled for until last Monday!! Crazy, right?
I have been pretty hard on a lot of the "artificial learning, machine intelligence, deep intelligence" stuff and I still think this is legit funny --
-- and I'm still going to be skeptical of anyone saying those terms (as we should be, of course) but I'm flipping through these spectra from this tool and this is one deep learning thingamabob that looks like its doing exactly what it's supposed to.
EDIT -- If you use spectral libraries in Proteome Discoverer -- go to the PSM level and double click anywhere on the PSM to open the normal menu you are used to. Now you'll find that this button is not greyed out. Click that and it will open your experimental vs library spectrum(a)(es)