Friday, January 28, 2022

WinO -- Prepping proteomic samples in bubbles in oil, cause why not!

Have you ever read a study and been both impressed by the ingenuity and quality of the work while simultaneously hating every well-written word and beautiful picture in it?  

I love WinO because it looks like a well-executed and extremely clever study. I also hate it because [excessive angry profanitities dedacted after I realized when I type profanities on this admittedly loud keyboard it scares the raccoon family that has set up shop in my attic. Turns out I haven't been hallucinating stomping in my attic, I just saw a tiny clumsy raccoon! SUPER cute, but I imagine having them up there is subideal for at least a couple reasons....] I thought that maybe, just maybe, at 17,832 variations of how to prep mammalian cells for LCMS based proteomics we'd finally gotten them all and we surely didn't need another way to introduce new inter-/intra-lab variability into our experiments, but here's another one! 

The illustration above pretty much explains the process. The aqueous suspension of cells and trypsin all conglomerate in the oil to get everything together so they can hang out. I'm fuzzy on how you get rid of all of the oil before LCMS. 

The results are seriously impressive. The titrate down the number of cells they use by FACs based cell sorting and look at them label free with scanning SWATH and with multiplexing on a Tribrid Orbitrap. Is it really smart and innovative? Yes.

Is it a beautiful, clear, well-executed study with remarkably well-displayed results? Also yes.

Is it a little frustrating that we have another sample prep method to keep track of that will undoubtedly produce a different distribution of detected proteins than the exact same cells prepped with another method? And will this method undoubtedly, at some point, undermine someone's credibility because lab A will use this method and lab B will do something else and the same data will go out to the same person and that person will be very confused about what is going on? 

Of course it is, but that shouldn't reflect on this study in any way because that is what LCMS proteomics has always done.

Am I going to be a vulgar hypocrite and try this method? Fuck yes I am. I ordered oil yesterday to set up some collaborator's samples right now. This is the best way of doing things, because I obviously didn't prep their cells like this last time, I didn't even know it was possible, so I don't even give any of you the chance to undermine me and my results, I'll do it myself.

After I try to get a picture of a baby raccoon. Dude was trying to get water out of our frozen pond, I think, so I'll need to put out a heated water bowl or something. 


  1. I never thought of ethyl acetate as an oil... wondering what chemists think about this!

  2. I never thought of ethyl acetate as an oil... wondering what chemists think about this!