Tuesday, September 10, 2019

Do you have TMTPro (TMT 16-plex)?!? Here is how you process the data!

First off. TMT and TMTPro and probably the word "plex" are the sole properties of Proteome Sciences. Trademark. Copyright. Whatever is necessary to keep me out of trouble. (Big R with a circle around it?)

Important stuff! (Don't sue me) We can plex 16 channels!!

Next -- HUGE shoutout to -- (Wait. Don't sue them either....I should anonymize the person who works for a company, shouldn't I....?) You know who you are, anyway! Dr. Secret Scientist 1 and Dr. Ed Emmott for the resources. I did none of this. Wait. I'll totally make the method templates for Proteome Discoverer because someone wrote me this morning and asked me for them. I'll contribute something!

#1: MAXQUANT for TMTPro?  Best of luck. Have fun. I won't help you at all with this, however...

Dr. Emmott (who will be opening his lab in 7 weeks in Liverpool) has made all the XML add-ins you'll need to modify MaxQuant to use these reagents and made them available via this DropBox.

(...thank you Ed! and good luck with the new program! Need help carrying boxes?)


This will require a couple of steps.

Step 1: You need to add the modifications to your instance of PD.

I recommend you update your UniMod

Both TMTPro 16 and TMTPro ZERO were uploaded today! I don't care about TMTPro Zero (sorry if you do, but you can figure it out. I believe in you! You're very very smart and people like you for obvious reasons.)

If you can't update your UniMod (offline or whatever) you can download this XML from my 100% totally nonprofit Google Drive thingy here.

Then you have to checkmark your TMTPro reagents, hit apply, and then in PD 2.2 I had to close my software and reopen it for it to take effect. Maybe in PD 2.3 as well.

Next you'll need to go to your Administration and import this quantification method (thanks Super Secret Scientist 1!)

Now you should have the picture at the very top of this way-too-long blog post!

16 quantification channels!

For proof that I've contributed something meaningful to human existence today. Here is the processing method for MS2 based TMTPro. You may note that the method name includes the words "probably wrong". I suggest you never get your methods from a completely nonprofit -- costs me a surprising amount of money each month to keep all these things going -- blog.

I wanted to make this as a reminder that TMTPro does not have the same mass you're used to at MS1.

And...according to Dr. Kamath (at a University, I checked, put them lawyers back on their leashes), who was just at a talk today about these reagents, you'll need to think about tuning your collision energy down for these reagents (hopefully to 27 NCE on a QE!)  I don't have details yet!

I think I'll be a reporter when I grow up. Today's blog isn't all that bad for a 9 year old.

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