I have an untargeted metabolomics dataset, where samples were collected over 4 timepoints (not repeated measures) from two groups of patients:

A) patients treated with placebo

B) patients treated with drug

1353 features were detected from LC-MS analysis, and I would like to do a two-way ANOVA analysis for each feature to see the effects of the treatment (placebo vs. drug) and time. I'd like to follow this ANOVA up with pair-wise comparisons to see in which timepoints the drug had a significant effect. I know that for the initial two-way ANOVA analysis I'd have to adjust for multiple comparisons (whether its Bonferonni or FDR correction) since I am simultaneously hypothesis testing on 1353 different features, but would I also somehow adjust the follow-up pair-wise comparisons to account for the 1353 features as well?

Thanks!