Thursday, November 26, 2020

Process TMTPro(16-plex) reagents in MaxQuant!


Huge thank you to Ed Emmott for posting these resources so I could get this workflow going this morning. 

Even if you just downloaded MaxQuant yesterday (1.6.17; i.e. "v.Mannly Wabbit"; [if you didn't know the newest version of R is called "Bunnie-Wunnies Freak Out", I think we could keep this trend going!]) you'll see that you don't have an option for TMTPro yet. That's no problem, but there are a couple of steps! 

You need: 

1) MaxQuant

2) To know where your MaxQuant folders are. 

3) This DropBox link from the Emmott Lab; you'll need both files (link here!)

4) This text file I made. Even though the title of the file is "probably wrong" it seems to work! Woo! 

Step 1: 

1) Make sure MaxQuant is closed. Check your version number that you are currently using. 

2) Find the folder where MaxQuant is actually operating out of. (You probably have a shortcut on your desktop and the actual folders are in your Downloads drive somewhere)


This is probably where you want to be. You want to now swap out the modifications.XML that is in your folder for the one from the Emmott lab dropbox. If you're a paranoid weirdo, just move the original XML file, but I've heard paranoia is rare in mass spectrometrists, so you'll probably just copy right over that old one while shouting "YOLO" or "Parkour" or something equally hip.

Now start MaxQuant. If you go to your Configuration tab, you should see at the bottom that the TMTPro reagent has been added! 

Now that you've got the reagents you can build your new Quan table or import the "TMT16_Ben_Probably wrong" Text file. 

You can also use the second folder in the Emmott Lab dropbox to file --> load parameters. 

And that's it. If you have the correction factors from the kit you purchased and you're a person who uses those you should punch those in. Otherwise you should be set. Looks like it works to me! 

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