Wooohooo! We knew this was coming for a year, but none of my stuff got accepted in it, which is totally okay. We rebundled a couple for Nature family journals where they'll probably get in. 😇 I did get to contribute by reviewing 3 or 4 of them.
Like most single cell proteomics papers out there, it's mostly perspetives and highlights and reviews.
Actually - this is funny - let's do it this way - here is each paper in the issue and the number of single cells that were analyzed. It's actually a whole lot better than I guessed! Out of 12 articles 7 of them acquired single cell data!
Take these numbers with a grain of salt - most single cell studies go to amazing lengths to not let you know how many cells that they actually analyzed. For some of these I had to go to the supplemental excel tables and for one I gave up and counted and recounted the number of dots on various U-MAP and T-SNE figures because I was too lazy to go to ProteomeXchange and count the .raw files.
Now - don't twist this - there is some great stuff here - but there is a misconception out there that because there are lots of single cell papers out there that every lab is doing lots of single cell proteomics or mass spectrometry. The perception that there is lots of data out there in the world makes it seem like it's easy. That means people who have never done it can get grants to do it and will spend the first couple of years trying to figure out how to do it.
Again - there is great stuff here. I haven't read it all, but I've read about half of these to some level and I'm already integrating findings here into my personal work.
I can't follow the scSeq meta-analysis papers - and they're just not in my area of interest in applying scSeq to my set of biological problems and interests right now.
The MALDI mass spec of the funny fish cells looks like an awesome study. Those fish cells might be bigger than frog eggs (200ng of protein) I honestly don't know, but 6000 single cells by MALDI is a fun read, right?
I've cited the EMT preprint at least 3 times already - it's a lot of fun, and I had an entire session that I named after the Payne lab perspective paper. The use of LysC rather than trypsin to simplify low input samples was featured on this blog last week and I just got a bunch of LysC in to see if their findings will translate to actual cells. Single cell lipidomics on the TIMSTOF is something that we've already looked at using this pipeline and I asked someone to buy me the software already. How you store single cells might have already been posted here - but it's 100% absolutely worth thinking about right now. And I've got to get cells to a collaborator and we're discussing whether we should fast fix them in formaldehyde now.
That was...a....rant..... but you should check it out!
No comments:
Post a Comment