In order to understand the molecular mechanism underlying the action of dPCIF1 in early embryos, we carried out co-immunoprecipitation (co-IP) assays followed by mass spectroscopic analysis using dPCIF1GFP-KI early embryos (0.5–1.5 hours). In this assay, we identified a large number of dPCIF1-interacting proteins. To search for the potential factor(s) with GAF, we performed co-IP assays of early embryos, followed by mass spectroscopic analysis, and generated a dataset for GAF-interacting proteins. To identify the site(s) of dPCIF1 phosphorylation, we performed phosphor-proteomics by mass spectroscopy and identified potential phosphorylation sites.