MaxQuant to MSstat question
Entering edit mode
Last seen 5.7 years ago

Hi There,

I had a question regarding using msstats from an output generated by

MaxQuant output on TMT results. The issue is when I use proteingroup

command on the output that I got from protein summarization command on


There are 2 type files hat are very similar, one file gives me the

correct proteingroup output whereas the other one looks like all SE,DF

pvalue,adj.pvalue columns are missing their values. I have tried it

many times over and over and the step before which is protein

summarization looks normal in both, but one file does not give the

correct protein Group.

I can send you the file that works ( GroupComparision-I) and the

other file that did not work(GroupComparision-M)

I appreciate any help. I can also send you all of my R commands



Yasi Jami

msstats • 1.0k views
Entering edit mode

First, I'm wondering whether you use MSstatsTMT package, instead of MSstats. MSstats supports DDA, DIA, SRM. MSstatsTMT supports TMT. If you use MSstats, please try MSstatsTMT instead.

And There are several points that are not clear to us. It will be better to share your R scripts with us in order to understand what steps you are not clear and which outputs you claim.

Hope that it can be helpful.

- Meena



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