Time-course study design annotation query

[ucl.c...@gmail.com]

Hello MSstats,

I am attempting to carty out a time-course MSstats analysis. I have attached a ppt file which displays my experimental design. I have 3 time-points, 2 treatments and 3 biological replicates of these. Using the supplementary section of the MSstats v4.0 paper, I made an annotation file where the 'subject' is my treatment (untreated v treated). I just wanted to check with you whether this is correct, please. I think my annotation file would just be looking at the time-point comparisons rather than the time-points/treatments comparisons?

Many thanks,
Amandeep

[Anthony Wu]

Hi Amandeep,

You're on the right track here.  I made adjustments to your annotation file and attached it as your original PPT.  

Based on your experimental design, you can create more specific conditions, like "time_treatment", and then use contrast matrices (see slide 2) to still make comparisons between different timepoints.  By incorporating treatment into your condition, you're able to block on treatment (see slide 3) when making comparisons between different timepoints, which should increase your power (assuming your treatment has an effect on protein abundance).  

Thanks,

Tony