Cassava is one of the major economic plants in Thailand, with Thai cassava production generating more than 3 million USD in exports in 2023. However, cassava production has been declining since 2021 due to an outbreak of Cassava Mosaic Disease (CMD), a serious disease affecting cassava plantations. The rate of infection has been increasing, partly due to the shortage of healthy cassava stems and CMD-resistant varieties. Using resistant varieties is the best strategy to control the spread of the disease. It is essential to develop methods that support breeders in shortening the time required to develop high-yield and CMD-resistant cassava. Our study aimed to determine signature peptide patterns for CMD resistance screening using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS).