Monday, December 11, 2023

Hypothesis shot down by one of the greatest proteomics papers ever! Typo??

Okay --- so I seriously think that something I'm looking at is a weird PTM that I'd never heard of before, which is a hydroxyproline.

However, the ProteomeTools project shot that down. They synthesized peptides with this mod on it and demonstrated that there is a very specific diagnostic fragment ion at -- 

In one of my very favorite papers of all time. Something that gets the crap cited out of it because it is AMAZING. You know it, but here it is anyway. 

And I don't see a matching fragment.  I see something close, and I checked my calibrations but it is definitely 171.076 something and I'm not running instruments here that can't tell 0.011 m/z apart. 

Because I'm stupid and had time during a seminar I went to PRIDE and downloaded the RAW files for this mod and I extracted the diagnostic fragment ion for 176.067 - and got an empty XIC. 

What? Right??  So then I extracted for 176.076 and BOOOOOOOOOOOOOOOOOM!!! A bunch of peaks! 

There was a small typo in the tables in the supplemental and that typo made it's way into the table and I think I've got a cool mod to show people that might explain why some proteins are being weird! 

1 comment:

  1. Hydroxyproline is mostly incorporated as an AA into collagen. There’s **tons** of it.