Donkey milk, similar to human milk in compositions, has been suggested as the best potential hypoallergenic replacement diet for babies suffering from cow milk protein allergens and a promising nutraceutical for aged people. In this study, label-free mass spectrometry analysis was conducted to quantitatively identify the whey proteins differentially expressed in high-milk-yield samples compared with low-milk-yield samples. A total of 216 whey proteins were identified, and 19 of them showed significant differences in high-milk-yield samples. Of these proteins, 16 were upregulated and 3 were downregulated. Differentially expressed proteins (DEPs) were subjected to intensive bioinformatic analysis. Results revealed that the majority of DEPs participated in protein processing in endoplasmic reticulum, estrogen signaling pathway, progesterone-mediated oocyte maturation, and PI3K-Akt signaling pathway. Functional protein analysis suggested that proteins functioned in binding, catalytic activity, molecular function regulation, structural molecule activity, and transporter activity. Our study was the first to analyze the whey protein profile of different samples of donkey milk and to identify candidate proteins that could be used to explore the molecular mechanism related to the yield traits of Dezhou donkey milk. This study provided the biomarkers for the selection of high-milk-yielding donkey and obtained valuable information for future studies. (C) 2018 Elsevier Inc. All rights reserved.