Wednesday, March 20, 2024

AI assisted proteomics - for everyone -with Ms2ReScore 3.0!


MS2ReScore is a great idea! Let's use Artificial Intelligence things to reanalyze our proteomics data based on various features of confidence to create bigger and higher confidence lists. It's free, too! see what you're dreading you'll see. "DOCKER"?? "git"?!?  

Great...another tool for bioinformaticians written for bioinformaticians that I could spend the next 3 weeks learning how to use if I didn't have 11 mass spectrometers that are running suboptimally, a grad student who still hasn't returned from Dubai and 3 grant deadlines. (These are only examples, but you get the point, time is limited). Could I just have a Windows installer for some of this magic? 

You can now! 

Not to be missed here is MSAmanda 3.0 which can be installed in PD 3.1 or newer and has stand alone versions for PC, Mac and Linux and can be ran through PeptideShaker. MSAmanda 3.0 by default outputs the features that Ms2ReScore uses to reassign peptide confidence.

When using MS2ReScore you also get cool HTML QC plots along with a bunch more peptides. When compared to MSAmanda + Percolator, it looks like a solid 20% increase on low abundance peptides. The authors use a nice SCP dataset that I'm going to assume came from Erwin Schoof's group and then they do a bunch of analysis that makes it look like these peptides are real and make sense in relation to the other peptides. 

I'm all for more data analysis tools, and I'm even more for them when I can just download them and run them! 

No comments:

Post a Comment