TMT 11-plex

[poori...@gmail.com]

Dear, Sir

 I use TMT-11 plex and run on q-exactive plus and search a data with a maxquant software.

I select on reporter ion ms2 as 11plex TMT  and found that all protein show 0 value in a reporter intensity corrected 10 11 channel.


Let me know if i set a wrong parameter on maxqunat.

Thank you

Pook

[David Bouyssié]

Dear Poorichaya Somparn,

Your problem seems to be an issue relative to the MaxQuant software itself.

The best I could suggest is to post your question on the MaxQuant dedicated Google group:

https://groups.google.com/forum/#!forum/maxquant-list

Maybe some other people active on this Q&A will give you a hint but I would this MaxQuant forum first.

Best,

David

[Vladimir Gorshkov]

Dear Poorichaya Somparn,

 As the first step, I would suggest you to check if the reporter ions for corresponding channels are present in the fragment spectra - i.e. open the files and inspect the region around 131.14 - there should be double peaks around 131.138180 and 131.144499.
If the peaks are there in spectra, blame the software (and if so, report the bug to the developers), if not blame your labeling method.

Best regards,
Vladimir

[Poorichaya Somparn]

Hi, Vladimir

I just saw the spectra already.  i see double peaks around 131.138180 and 131.14449.

Now, I use Proteome discovere 2.1. I got intensity of all channel

I will  report the bug to the developers


Thanks.