Saturday, October 28, 2017

Where do you get all those values for proteomics ruler calculations?

The proteomic ruler approach has appeared a couple of times on this blog.  While incredibly cool, when you start trying to do it you may run into this issue -- "where the heck do I get these total intensity values"? The authors are using MaxQuant, but maybe you're using Proteome Discoverer? And you don't want to go back to the RAW file and start taking averages, right?

BIG SHOUTOUT TO DR. CLELAND at the Smithsonian! We were having lunch and he told me exactly where you get the numbers you need!

If you are using PD 2.0 or newer (you should be using 2.2...) there is a post-processing node called Result Statistics.

I always throw it into my workflows -- cause it doesn't seem to add any time to the data processing and it adds a tab of data, but I've honestly never used it for anything.  AND EVERYTHING YOU NEED IS HERE!

For example, if you want to normalize your data against the total area or intensity of every feature identified in the entire dataset?

It is on row 612!  There is so much information here, including the stuff you'll need to start calculating your absolute protein abundances.

1 comment:

  1. Very cool. This is something that I was searching or at least trying to apply with my data. Now I can work with it!

    Thank you!