Monday, July 11, 2016
Super in-depth analysis of FASP shows optimization is sample specific
Filter Aided Sample Prep (FASP) has been surprisingly controversial. Groups rapidly started pointing out limitations to the technique. Wow, I just did a quick check and I have posted at least 10 different papers on this blog where people have improved FASP in some way or another.
So...Jacek R. Wisniewski (who knows something about the topic, I've heard) went through two variations of FASP -- regular and MultiEnzyeDigested MED FASP -- and made possibly the definitive guide on the topic.
You can find it at JPR here.
What did he find out? That it might not be something as simple as --"Eureka! This is the perfect FASP protocol"
How well he did with each technique had a lot to do with what he loads and how much. Fortunately for us, however, he did all the work!
Personally, I think these findings are disappointing. We need to standardize our protocols from lab to lab if we're ever going to shake the "proteomics isn't reproducible" bologna that has shot down more than a few of the nice grants y'all are writing.
That's science, though! As much as I don't like these results it sure seems like Jacek has done a thorough job and this is quite convincing. Maybe we can circumvent this by optimizing FASP protocols for the pure discovery work and work on a universal sample prep method for getting this reproducibility monkey off our backs?