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

msstat.

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

Thanks.

Regards,

Yasi Jami