Sunday, April 3, 2022

The TIMSTOF SCP Prototype paper is out!


I haven't had a chance to read this one all the way through yet, but we'll be talking about it in lab a lot when everyone gets back from Experimental Biology but I've read far enough to know that a lot has changed since the original preprint (almost 2 years ago? I think it was right around ASMS 2020?) 

I had a peer reviewer around 9 month ago talk about how much better this data is than one of our single cells studies we had submitted and since other authors had to sign off on my response I couldn't type what I wanted which was: What an amazing an intuitive assessment! I'll be right back after I cut up my Department Chair's 10 month old, $1.3M instrument, add a vacuum pump, a right angle to the ion beam, fabricate an ion transfer tube with massive hole in the center and modify the tune software to accept all these changes! Thanks for helping!

The fact of the matter is that this is a really nice study. The now that we do have the TIMSTOF SCP which is based on the prototypes much of this data was generated on and we have this increased signal and possibly even dynamic rang we're definitely going to try this sample prep and pasefDIA based approach. (We're in early learning curve....I've got 4 files that are worth keeping so far, but I'm getting there!)

If you've spent a lot of time on the preprint and wonder if the accepted version is worth your time, I've found a lot here that either I forgot, or I think is new. You aaaaaalmost get a MaxQuantDIA vs. SpectroNaut vs DIAnn here. What you get is a very polite statement that this wasn't intended to be a software comparison, but...we'll...only show or talk about data from DIA-NN for the rest of the paper....(I forgot the nomenclature for the software). 

Again, it's a really nice study and a really impressive tool and there is some really smart work here comparing single cell seq with their results. I do think it is critical, though, to keep in mind that the majority of mass spectrometry data that has been generated on actual single human cells has been generated on the nearly 10 year old Q Exactive Classic platform. You aren't locked out of SCP if you've got older hardware. The real challenges are getting your cells prepped and figuring out what to do with the relatively low coverage proteomes of 1,000 things that should be a lot more similar than the data suggests they are. 
And maybe, I guess, convincing some reviewers that it's okay to use the hardware that you actually have access to. 

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