WHOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAAAA!!!!!
Dataset for reanalysis alert!!
EDIT - EEEEEEEEEEEEEEEEEEEEEEEEEEEEKKKKKK! I can't find the data files. Contacting authors now.
I have some 100SPD files from Matt Foster's Astral and I think they're like 8GB? So....8GB x 36,000? Is that 288 TB? It might just be uploading and they wanted to preprint something this year?
Mann lab optimized perchlorate based enrichment to get a super cheap sample prep method giving them about 2,000 proteins per sample in human plasma. Then did 36,000 of them?!?! No nanoparticles? Off the shelf stuff? I need to read this, but - whoa.
There's a number of issues with this preprint. Of course, no data availability as is now somewhat normal for preprints. But I see lots of claims with no evidence...
ReplyDelete2,000 PGs claimed, but show 1,315 in data which isn't too different than PCA... Also a bit concerning that in 5 samples they show 2500 PGs aggregate, which suggests high data heterogeneity with either PCA-N or PCA method.
Neat CVs were in line with expectations but PCA-N was 2x greater magnitude, resulting in reduced biological signal interpretation on median robustness features. Matched features would have been interesting...
13k sample preps per day seems a bit exagerated too. It would require massive automation and technician effort to balance all the incubating plates. Krakatoa type samples may be more realistic one day. Maybe this was a commercial group sticking their hand it to say we can do 1/3 of the year long acquisition cohort in a day... Also claiming 1536 plates but not showing it...
Frustrating that a non openly available international standard was set and used again. I realize they are important, but accessibility is lacking and should be paramount to standardization.
Would also love to see the actual methods they're using for batch correction. It's a glaring hole in their methods.
Hoping this paper gets a massive transparency revision in the peer-review update.