Tuesday, July 25, 2017
Dinosaur protein sequencing!
I swear, I would absolutely credit the person who photoshopped this together, but Google Images doesn't know who this mastermind is, just that the original image was on Tumblr here.
Credit for finding the paper I'm about to ramble about goes to ProteomeExchange, where I was just sleepily browsing for some new RAW files to torture my PC with -- and BOOM! Awesome paper with an okay title.
Improved title suggestion: WE TOTALLY SEQUENCED SOME DINOSAUR PROTEIN WITH AN FTICR! DOWNLOAD THE DATA, WE AREN'T MESSING AROUND!
First off, this isn't novel. Previous studies by some of these authors and others have been seen before. The one that first comes to my mind is the 2009 Science Study. However, this was met with a pretty serious degree of controversy. (Side note: I consulted on a potential dinosaur protein sequencing project maybe 5-6 years ago that looked super positive, till I BLAST'ed all my de novo results. Getting clean and pure samples this old is REALLY hard)
So. Why this paper? Because it absolutely supports the 2009 study! The protein removal process was streamlined and improved to minimize handling (the Sample handling and anticontamination procedure section of the Materials and Methods is intimidating). Even better, the improvements in the available sequences to compare this with -- and the improvements in proteomics algorithms makes this all more valuable. Even finding one new peptide sequence can improve our understanding of dinosaur phylogeny -- and they find a whole lot more than one!
It has got to be awesome to go through so much work -- where you've got to have some doubt in your mind if something is gonna be there -- this is a 60 million year old rock -- and then...
BOOM! Clean blanks and Dinosaur Protein!!
Its 8 o'clock! Time to wrap this up. They use a 12 Tesla LTQ-FTICR and employ both PEAKS and Byonic to sequence the results. The search tolerances are kept extremely tight and not one peptide is reported with an MS1 discrepancy over 4.5ppm. In fact, only 5 fragments are reported in the whole study with an MS/MS tolerance over 20ppm.
They use the collagen sequences in a variety of ways (comparing to known modern and prehistoric collagen sequences) to improve our knowledge of the phylogenic trees and evolutionary placement of this and other dinosaurs.