MaxQuant to MSstat question
0
0
Entering edit mode
@yasamanjami-18264
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

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

msstats • 1.0k views
ADD COMMENT
0
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

 

ADD REPLY

Login before adding your answer.

Traffic: 1212 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6