First of all I have to say that I am newbie with Max Quant haha. I have been using other Proteomic software like Proteome Discoverer and Scaffold.
I have got 6 samples ( 3 control biological replicates and 3 treated biological replicates). Each control has got 9 fractions.
My question is about the ratios. In my experiment I want to compare Control samples with Treated Samples. Usually, in Proteome Discoverer and Scaffold, I can have a specific column with intensity ratios between samples (Example. Control vs Treated).
However, in Max Quant I can not find that option. I only have the column with the LFQ intensities. Is there any way to calculate that ratios?