Our spectral matching tools are going into some unprecedented territory right now in terms of the ridiculous power that they have. I doubt we'll ever get to a point where we disregard SeQuest and what it has continued to evolve into, but -- holy cow -- there is some amazing stuff out there right now.
A new entry in this amazing category is Open-pFind. Here is the bioRxiV link, but it's now in Nature something or other (can't find the link yet) -- which seems to be advanced beyond the preprint entry.
pFind isn't new, but this is pFind 3.1. As far as I can tell, a totally free GUI (you just have to go through a licensing procedure so they can keep track!) that you can get here.
What's it do? Well -- like the other entries in the category (the ones I use the most right now are Fragger/FragPipe and MetaMorpheus, but there are obviously others!) pFind doesn't care what modifications you're looking for. It blows up the search space to a huge level and then starts pulling out the modifications. You can find what you never thought to look for, in large scale.
It looks like it uses a different type of mechanism for making matches than the others. I
You know what this blog needs? A DEATHMATCH. There hasn't been a software DEATHMATCH in forever. Time to get a great dataset, these 3 software packages and pit them against one another in a vaguely scientific and moderately unbiased manner. Gotta come up with some rules, though....
Don't be distracted by my rambling --- there is some serious important stuff to learn in this paper. Their tests are extensive and show both the power and weaknesses of other programs out there.
There is also some surprising insights (to me, at least) into the "Dark Proteome" stuff. And....well ....even about trypsin. It only cuts K/R, right? Right??
This is a great paper that deserves some serious attention.
Shoutout to @Karl_Mechtler for tipping me off to this great resource!
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