Longitudinal liver proteome collected at 4 time points (d -21, +1, +28, and +63 relative to parturition) from Holstein cows treated with abomasal infusions of coconut oil (CTRL) mixture of essential fatty acids and conjugated linoleic acids. The file contains protein descriptions, raw intensities, associated gene names, peptide count, differentially abundant proteins assessed by repeated measurements ANOVA-simultaneous component analysis, and Gene Ontology (GO) and functional enrichment analysis during the transition to lactation, between CTRL and EFA+CLA, and their interaction.