An approach to collect and interpret results from Y2H screens uses high-throughput next-generation sequencing technologies. In particular, this system is appropriate to generate comprehensive profiles of protein-protein interactions (PPIs), allowing also a side-by-side comparison of specific PPI patterns with that from control samples and allows a direct comparison of PPI patterns displayed by proteins in their wild-type and various mutant conformations. While sample preparation relies to the most part on established transcriptome and RNA sequencing procedures, this invention also encloses a specific DNA preparation step to sequester irrelevant and contaminating sequences from the sample.