Monday, March 24, 2014

PTMrs!!! Confident site localization of all PTMS in Proteome Discoverer!


I have yet another awesome new node that you don't have!  If you are interested in any kind of PTM, you are going to want this.

You know PhosphoRS.  Site localization probabilities for your phosphorylation events.  Last week, Karl Mechtler (from the lab that wrote PhosphoRS) contacted me to see if I wanted to check out his team's new node, ptmRS.  Yes.  Yes, I do.

Guess what it does!  Site localization for any post translational modification that you give it.  I'm serious.  I dropped it in this morning (easy install, didn't even look at the instructions), threw in a HeLa digest run from an Elite, gave it Phosphorylation and ubitiquinations to look for.  6 minutes and 18 seconds later, I have this report to look at.

I have localization of my few phospho events as well as a few di-Glycine (left over from ubiquitin cleaveage?) and confident localization.  I went after the lysine di-Gly first cause they're kind of low-hanging fruit (we should only have 1, maybe 2 lysines per peptide, right?  How does it do with some great enriched data?  I just found some on one of my spare hard drives.  Stay tuned.


  1. Nice piece Ben.

    >>> Where do I find / get this node ???



  2. Mark,
    Thanks! I'm sure Karl's team will be putting it up on soon. I think its still in the testing mode, but I've been running it like crazy and I've yet to find a glitch. You might be able to talk to them for an advanced copy.