Pharmaceutical companies are being forced by market competition to find new ways of novel drug target screening instead of traditional methods. The completion of human genome sequencing has provided a flood of new information that might help identify potential drug targets. Finding promising novel drug targets from this flood of information remains challenging. For de novo target screening, the interactions between a drug and cellular components must be comprehensively characterized for better understanding of the pharmacological activities of the drug. The multidisciplinary chemistry-based functional proteomics can be used to elucidate the interactions, because it provides a method to focus initial new drug target identification towards proteins that are more easily validated and most likely to be effective, thereby creating a higher potential for success. This review covers major chemistry-based functional proteomic approaches and highlights their recent advances in applications for novel drug target screening.