We developed a method for comprehensively profiling drug-protein interactions using micro-column affinity purification(AP)combined with label-free quantitative(LFQ)proteomics as well as the statistical and bioinformatics analysis.FK506 was used as the experimental model for proof of concept.The true interacting proteins were distinguished from the background proteins by their fold changes of FLQ intensities combined with p-values.Totally 116 FK506 interacting proteins including 5 known target proteins were identified.The method was validated by using the LFQ intensity of the endogenous known drug targets together with statistical analysis.We demonstrated that the micro-column-based affini-ty purification in combination with LFQ proteomics provides a highly reproducible and robust approach for profiling drug-protein interactions.