I haven't seen the .d files for this yet (I'm not sure if they're up?) but I'd really truly love to know what people who do plasma/blood proteomics all the time think of this new study!
Somebody put this up on r/proteomics to start a conversation about it if that's a format of social media you use. I'm thinking about this big plasma cohort I was on the fence about taking on and whether this simplifies it and gets the cost down to where I could do it?
This interesting! But it was done by several groups (maybe differently/different precipitation reagents) in the past. We tried something similar to this paper and it works. The issue we had was to make it operational and robust. The pipetting of the supernatant and the potential remaining aggregates in it was a problem. There is also a need for automation, because incubation time, pH and temperature can have an effect on precipitation kinetics.
ReplyDeleteUpside: fast, cheap and easy to reproduce.
Downside (like any depletion method): various partial protein precipitation methods will give you a different protein list. You always build a bias doing this....
Ultimately you may need to use a strategy like SEER.Bio proteograph and combine methods to reduce the bias.
Downside with Perchloric Acid: It's a nasty acid!
In house, we have a solution we believe to make it robust without the need of pipetting and probably no need for using perchloric acid as a precipitant. We need to further proof it.
A few refs
https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00232
https://pubs.acs.org/doi/10.1021/acsomega.0c04568
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166306
https://www.longdom.org/open-access/protein-fractionation-for-quantitative-plasma-proteomics-by-semiselectiveprecipitation-32775.html
https://pubs.rsc.org/en/content/articlelanding/2015/an/c5an01560j
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9239184/