Saturday, October 5, 2019

Proteome Discovererer 2.4 Scripting nodes!!

Yes -- Perseus has basically always been able to interface with external code and programs and has ugly little icons to link all this stuff together -- but Proteome Discoverer never has without being in the ultra special developer's club!

TADAAAAA!!!!  The Proteome Discovererererererererer  2.4 Scripting nodes!


I had to follow this poster that isn't quite exactly what was commercially released, but close enough to be helpful.

I still can't make it do all that stuff.  But I made it do something!

First of all -- there are two scripting nodes -- one in the Consensus and one in the processing.

You can do simple things with it like have it send whatever data you want to different executables.

Here is the super easy example (click image below to expand)

In this case I just had it send the protein descriptions to NotePad. TADAAA! Totally dumb, right? But could you do that before? I couldn't.

But you can send stuff from Proteome Discoverer to R or Python or other things if you want. For R, you're going to need a few things first.

You're going to need R Studio (which will require R)
You're going to need an interpreter to convert JSON files into R (RJSON can be found here)
It appears to require some other tools, but it will tell you when you go to install it.

Actually install.packages ("RJSONIO") seems to do it, but it complains about something and now I forgot what that actually was.

Okay -- so sending stuff out of PD is cool -- but what is really really cool (and beyond me at this point) is the ability to do a calculation and bring it back in.

The example I'm working on -- I'd like to know my peak width in every file. If you use Minora you get your Apex RT, you're left RT and your Right RT. In minutes. I'd like to take the absolute value of left vs right and multiple it by 60 and bring in a new column that has my peak width in seconds.

I'd never ever have been able to do it before, but in Proteome Discoverer 2.4 -- I'll still probably never be able to do it, but the tools are there!


  1. Why is the path to executable pointing to notepad.exe?

    1. ...because that was the funniest thing I could find the .exe for...