Updated publication reference for PubMed record(s): 31645615. Advances in gene editing now allow reverse genetics to be applied to a broad range of biological systems. Ultimately, any modification to coding sequences requires confirmation at the protein level, although immunoblotting is often hampered by antibody quality or availability especially in non-mammalian species. Here, we show that Sequential Window Acquisition of All Theoretical Spectra (SWATH) - Mass Spectrometry (MS) is a robust antibody-independent alternative for monitoring gene editing at the protein level and concomitantly defines proteome responses which may provide pertinent biological insights.