Although the focus on analysis of protein sequence has been one of regular approaches in modern biosciences for the past several years, similar methods have not been widely applied in ancient residue research. The present work proves the capability of LC-MALDI-TOF-MS/MS to identify the milk component preserved in ancient food remains, and clearly discerns the origin as well. Additionally, it is suggested that alpha S1 casein could be used for discrimination of the origin of milk in ancient residue. Moreover, considering both of the lower detection limit and higher accuracy, those involved in this study believe that not only the visible residue, but also the invisible residue, such as the protein absorbed in pottery, could be identified by proteomics methods. Furthermore, the results imply that animals such as goat/sheep and cattle were raised for milk, which enriches the understanding of Subeixi culture (cal. 500-300 BC), the furthest eastern location of prehistoric milking up to date.