This dataset contains the enriched protein interaction candidates identified by immunoprecipitation–mass spectrometry (IP–MS) using CrETT (Capsella rubella ETTIN/ARF3) as bait. The data include protein lists obtained from two experimental systems: (1) transient expression of CrETT in Nicotiana benthamiana epidermal cells and (2) Capsella rubella gynoecium tissues. Samples were subjected to either mock treatment or indole-3-acetic acid (IAA) treatment prior to protein extraction and immunoprecipitation. The dataset provides the identified and enriched interacting proteins, together with quantitative information generated from mass spectrometry analyses, enabling comparison of CrETT-associated protein complexes under different auxin conditions and biological contexts.