run the MaxQuant for TMT data

[Proteomics_lerner]

Hello,

I want to know how to use MaxQuant for protein identification of a TMT data?
Is there any tutorial for these type of data analysis ?
Thanks

[Mohamed Elzek]

Hello everyone,

I have performed a TMT 10 plex analysis using MAxQuant 16.0.01 following this protocol https://www.ncbi.nlm.nih.gov/pubmed/27809316. However the identification looks pretty ok however maxquant always reports reporter intensities as zeros. It seems that there is a problem in performing quantification. Is there anyone who has more experience can point out the solution for this?

Thanks in advance!!

Mo

[Torsten Mueller]

Hey everyone,

a while ago I had the same issue. Did anyone by change find a solution for the reporter ion intensities being zero?

Thanks in advance,
To

[Kerri Ball]

I have seen this issue.  There are both maxquant version issues and download/install issues.  For example, version 1.6.2.1 didn't work (all 0s) when I downloaded and installed it the first time, but it worked the second time.  Version 1.6.3.4 worked the first time it is easier to add the TMT isotope distribution errors with this version.  I have also had the issue were I said MS3 but it was actually MS2 data collection.  So you should double check that too. Good luck!

[Nimai Charan Mahanandia]

Respected Sir,

Can you solve this problem TMT data analysis in MaxQuant?

I am also facing same problem in MaxQuant.