Sunday, March 8, 2015

Quantitative digital proteomics maps from biopsies

Alright...there is a ton of interesting stuff in this paper....and, in general, I don't know exactly what to think of it yet.  But I'm gonna tell you about it anyway!

What is it?  Its this paper at Nature Medicine from Tiannan Guo et al., and it entitled: "Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps."

What did they do?  They took biopsies and digested them using something called a Barcocycler. Google Images tells me it looks like this.

And the first website to pop up describing it (here) describes it as a cell lysis technique using barometric pressure.  Considering it includes the word "cycler" in its name, I have to assume it is a more complex piece of equipment than the pressure bombs we used in Microbiology class for chemical free cell lysis.

The authors of this paper describe their digestion method as one that minimized transfers.  They put the biopsy tissue into the Barocycler tube and it appears to stay there throughout the several steps until they have nice digested peptides at the end.  I'll take that.  Lets minimize some variables!  Anyone know how much one of these costs?

Now, I don't know anything about pressure cycling digestion.  Maybe its massively superior.  I'd love to see more data.  For a more conservative person, I would argue that there are other devices out there, like the stuff from Perfinity that also minimize transfers and have a good track record for reproducibility in the literature.  I'd be interested to see how these compare.

The resulting digested samples where then ran in a data independent acquisition style experiment (called SWATH) using 25 Da windows.  The resulting MS/MS files were processing with Open-SWATH against established libraries.  They also use a decoy database to work in an effective false discovery rate metric.  They do all of their statistics using established available R packages, including aLFQ (which you can find, open access, here...oh...which I guess these authors had a hand in developing as well, I don't know how I missed that before.  Nice package!)

The output?  Some really nice data.  Quantitative analysis of ~2,000 proteins per biopsy.

Now if you're thinking. 1mg of protein and they only got 2,000 proteins?!?!  How the heck did this get into Nature Medicine? Is it 1995?

Ummm...did you see the awesome title...and the nice heat maps...?

Update 3/10/15:  A reader whose opinion I  respect wrote me and said this regarding the Barocyler:
 "I used it for a couple of months looking at how well it does homogenizing small amounts of insect tissue. It works, and works well."

Might be worth checking out, especially as it sounds like evaluation of the instrument is a possibility!

1 comment: