Monday, April 11, 2016

iPTMnet - understand PTMs in biological context!

Sweet! So you found a post translational modification in your big 'ol dataset. What do you do next? Great question!

Why don't you check the protein in iPTMnet (here!)?

iPTMnet is a compilation of proteins and their annoted PTMs from all sorts of organisms. It is super easy to use and brings data real fast.

Punch in the name of your protein of interest, limit it to your organism (if you want to) and it'll show you all the PTMs that people have found for this protein and where they are located.

It'll also break them down in a table and have a link to where they got the data for that PTM.

It is worth noting that most of the PTM work in the world is still phosphorylations. And PhosphoSite is probably the best place to deposit that kind of data, so...when I punched in a couple proteins off the top of my head --well...I just got the same data I'd get punching this protein name into PhosphoSite (every modification listed just hyperlinked into PhosphoSite. But there are groups out there working on all sorts of PTMs and we're going to see more variety in PTMs in our databases soon!

The interface is nice enough to be a go-to AND it is less counter-intuitive.  When Dr. Collaborator asks for advice for where to get more information on her ubiquitinationed peptides you found it'll sound more linear to recommend she check it here!

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