We're all using deep learned machines for artificially inflating our intelligence in some way or another right now, but a lot of those thingamabobs are kind of convoluted.
Have you ever wished that you could just type in just one peptide sequence into a handy little box for a quick additional confirmation that what you are looking at is what you think it is? I sure have!
I made a brief visual tutorial here.
Did it just predict the fragmentation of a phosphopeptide for me?
Heck yeah it did!
Did it do a good job?
There is plenty of documentation on this awesome Github!
What I've found by trial and error is that you have to use all capital letters for your modification, and you want to get the square brackets and not whatever not square brackets are called. And it will do at least phosphorylations and lysine acetylations. I chatted briefly with the author [Sebastian Paez (@jspaezp1)] and he's looking for community feedback to improve it, so check it out!