Subject area	Biology
More specific subject area	Proteomics, Protein–protein interactions, Arabidopsis thaliana, plant biology, circadian rhythms, photoperiodism, affinity purification, mass spectrometry
Type of data	Table, figure
How data was acquired	Mass Spectrometry (LTQ-Orbitrap Velos Pro)coupled with HPLC (U3000 RSLCnano HPLC)
Data format	Raw, processed
Experimental factors	10–12-day-old seedlings of Arabidopsis thaliana expressing bait proteins were grown under diurnal conditions (light: dark=12 h:12 h with constant temperature (22 °C) and sampled at ZT12 (12 h after light is on).
Experimental features	FLAG-His tandem purification using magnetic beads coupled with on-beads trypsin digestion. High-resolution mass spectrometer coupled to nanoHPLC for protein identification and quantification.
Data source location	Saint Louis, Missouri, USA
Data accessibility	Data are within this article and have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002606 athttp://www.ebi.ac.uk/pride/archive/projects/PXD002606or dataset identifier PRIDE: PXD003352 athttp://www.ebi.ac.uk/pride/archive/projects/PXD003352