Transfer single cell peptides all over the place with NO peptide loss at all!

 

4 people have sent me this new preprint and I've had to go "...oh...it's in my draft's folder..." but the power went out in my building while I was at a conference and it's sort of a mess and I'm grumpy, so Imma post this. 

So...sometimes I see these papers where someone does something like - 

1) Get better results than anyone in the world has ever gotten with that instrument (or at all) 

2) And when you do that...if you don't make the data publicly available, I have to think....

Let's do background first! 

THE number one challenge in single cell proteomics (or any low input stuff) is informatics, probably, but right there with it is just protein and peptide loss through plain old surface adhesion stuff.

If you put a 200 picograms of peptide diluted in a 4 microliter droplet in a 384 well plate you'll lose about 30 picograms of that material to that plate surface (say..125uL well volume). It's just gone and DDM will help, you you aren't getting that back. Pick that up in a DDM coated pipette tip and you'll lose another 20 picograms. If you take that droplet and you add enough liquid to it to allow it to effectively vortex it and then thoroughly vortex it  - you'll lose a whole lot more! Peptides stick to plastics.

Even when we're dealing with hepatocytes at 400 picogram of protein (single nuclei) we're probably not getting 200 picogram to the instrument because with our workflow. Loss loss loss. And you can buy a more sensitive instrument for $1M or you can cut your losses by 30% and get the same thing.

In this study - this group transferred a single cell peptide load over and over again! Like 4 times! (four, 四, cuatro) and then - got more proteins per cell than anyone has ever reported on that same instrument with nanopots (single transfer, but exceptionally low loss during prep) or with single well digest, pickup, load, on that same instrument. They just pipetted the cells from here to there and used magnetic nanoparticles and then desalted and then transferred it again and then still got huge numbers. That's a big big claim and you generally expect big evidence to support something like that. But...when there isn't any....it's hard to say or think nice things.