This is my problem. I have data from label-free proteomics experiment. I have 4 strains with 5 time points in each and 3 replicates. One of the strains is a negative control and expresses nothing, while 3 others are induced to express different proteins at time point 0. Overall I have complete data (all strains, time points and replicates) for around 1000 proteins.
What I'm interested in is finding which genes have significantly different profiles of expression in the other 3 strains compared to negative control. And I'm not sure what to do? Should I just make a t-test of negative control vs. each of the strains in all 5 time points? Or is there a more sophisticated solution?