Statistical method for high throughput NGS data

I have a high throughput NGS data (peptide sequence and peptide count). I have cleaned my data, and now I want to apply statistical test on this data. I want to understand which statistical method I should apply and why?

There are three samples for each patient (before treatment, after treatment, after protein incubation in sample after treatment). Patients were treated with two types of drug.
Hypothesis1: Patent treated with drug one vs two develop inhibitors.
Hypothesis2: Why of hypothesis1.