Ecumicin and Cyclomarin A (CymA) are known antimicrobial compounds that target the NTD of ClpC1. In proteomics analysis of compound treated M. smegmatis, two novel protein, ClpC2 and ClpC3, have been identified as strong interactors of those compounds in addition to ClpC1. In this study we used PRM to monitor the levels of ClpC1, ClpC2 and ClpC3 over time after treatment with CymA or ecumicin or CymA-based BacPROTACs.