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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  2. Hi Ben thanks for the post! I followed your workflow and used the Emmott lab files to run my 16plex TMT data set in MQ. However, when I move to Perseus I have plenty of proteins identified but none are quantifiable ( all my reporter ion intensities are 0). Have you run into this at all/any idea what I'm doing wrong?

    Thanks for the help,


  3. Hi Ben,

    Thank you very much for the post, it is really helpful. However, when I tried to normalize my TMT samples based on reference samples/ channels, I noted that it is only possible to set the reference channels up to channel 11. In the dataset that I am using, the reference samples are in channels 12 up to 16. Do you maybe have a trick or a solution for this problem?

    Thanks in advance!

    Kind regards,

    1. Nuts, sorry to hear that! I don't have a trick, unfortunately. I bet you could adjust the normalization with Perseus, but I'm not skilled enough with it to try.

  4. Hi Ben,

    thanks for this, it worked really nice with newer versions of MQ. However, I could not replace the modifications.xml file in the version without getting an error (I assume the structure of this file changed a bit in the newer versions). Can you tell me how to modify the .xml file myself? Would you do it in Notepad?
    Thanks for the help!