Monday, September 22, 2014

It was cool while it lasted -- the end of LC-MS/MS based proteomics

EDIT:  Just to clarify, I put this title in to be funny.  When I saw the relatively huge number of hits this entry has received in the past few days, I figured it would be a good idea to throw in this edit.  LC-MS/MS proteomics is obviously, not going anywhere.  It is worth thinking about, however, that this isn't the only way we can do proteomics.  Protein arrays are gaining speed and improving in quality every day and this method for amplifying DNA tagged proteins is very very interesting for proteins that we can tag.

Genomics techniques are more sensitive than proteomics techniques because DNA can be amplified.  PCR didn't get the Nobel for nothing.

For years people have been working on "something like PCR" for proteins.  Because that is really what we need to get down to the bottom of the dynamic range pit.  But proteins don't like to amplify.

So what if you just tag the protein with a DNA barcode?  You make the protein have a little specific DNA tag, then you use all the amazingly sensitive and specific tools the genomics people have been using forever to 1) concentrate the proteins with matching tags and 2) amplify that tag.  You'll know what protein is present and how much you started with!

The authors of this terrifying paper demonstrate that this approach works on both large and small studies and describe the benefits and limitations of their techniques.  One of the limitations?  It would be tough to DNA barcode every human protein in a living person.  For now this technology is limited to small well-known experiments.  So maybe LC-MS based proteomics will survive, but this approach (if its valid...getting too skeptical about what I read....) sure is an interesting new tool to put in our belts!

By the way, I'm really sleepy (long day of traveling thanks to high winds on the coast) and I'm just being alarmist.  You can check this paper out yourself here.

No comments:

Post a Comment