Sunday, June 26, 2022

Multiplex 29 proteomics samples by using every reagent!


Around my ever increasing horror watching my country, the one with the most nuclear weapons, fall every day to the demands of a minority of people who live their lives by literal interpretations of very small excerpts of an ancient and poorly translated book that they clearly have not read, it is hard to focus on science, but for my sanity I'm going to try anyway. 

When I saw this new title I was SUPER EXCITED....

It is tough to create new multiplexed reagents, while more than the ones we commonly talk about probably exist the ones that we talk about are protected by some extremely observant lawyers. As I might have mentioned before, I've experienced the keen observation skills of said lawyers first-hand and what I type in these boxes has to, at some level, be guided by considerations of what might end up making them get all jumpy and litigationy again. 

The number "29" probably should have tipped me off prior to the abstract that something fishy might be going on here. We've got 11-plex and 18-plex reagents now. Which to use? 

At first you might say, as I did, f******************k thaaaaaaaaaaat. How would you process the data? Why would you ever double your reporter background interference from coisolated peptides? 126-131n literally just doubled. 

Okay, but somehow the data looks good here. Maybe this is worth reading more of? They probably used real time search based MS3 or super tight ion mobility? Nope, they used a Q Exactive HF with 1.0 Da isolation windows an the JUMP masstag software

The authors used a two proteome digest to pressure test their quan with E.coli labeled with one multiplex reagent and human brain labeled with the others and -- somehow -- the quan doesn't look bad. I don't think that with my software of choice that I can replicate this. I'd need to have my 4 tags that are usually static set as dynamic which would do wonders for my search space and FDR and it would take a lot of post-processing to get this sorted out. I might be wrong, though! And -- if you're in a pinch, maybe this is something to keep in the back of your mind? 

No comments:

Post a Comment