Friday, December 16, 2016

Clean out the litterbox and get rid of some false discoveries!

At first glance, this figure seems a little silly and maybe alarmist, right? I retweeted it, but it didn't immediately crack my top10 list of papers that I need to give more time. As I passed it by a second time, I thought -- the editors at JPR must have seen something in it AND the title is funny, but now I highly recommend you read it!!

It is Open Access too!

Here is the idea in a nutshell --> we often use chemically modified trypsin that isn't supposed to spend all it's time digesting itself. But...when these researchers go to look at big public repositories and then take into account the modifications present on the trypsin that was used in the study -- they find a lot of peptides that sure look like they came from the trypsin.

Interesting tidbit:

I did not know this at all -- trypsin is trypsin, right? now I'm super depressed. I'm thinking now I've got to add a bunch of dumb PTMs to my search database or run a separate search algorithm with a bunch of PTMS added to my cRAP database and combine the results downstream...

Thanks, Billy! I can't wait to hear about it!

The solution these researchers propose? A new amino acid!  They add in a new amino acid "O" or "j" depending on the algorithm and give it the mass 156.12571 -- the mass a dimethylated lysine should have and then apply the new amino acid to the sequence of the modified trypsins. And...voila!...litterbox cleaned!  (They find they improve their true and false peptide identifications in every sample and search engine they test!)

While on the topic, I'd like to remind you cat lovers that Toxoplasma gondii is no joke.  You don't want to end up like this...

Did I read this paper partly because I really wanted to integrate this video onto the blog somehow? Umm....

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