A matrix that enabled chirality and structure-selective detection in matrix assisted laser desorption ionization mass spectrometry (MALDI MS) has been developed. Molds of L- or D- alanine were made on a thermoreversible polymer (polyvinyl methyl ether) with 2,4,6-trihydroxyacetophenone, and this was used as a matrix. Separate detection of one optical isomer of alanine was realized in MALDI MS. This technique was also applied to the detection of trisaccharides having the same molecular weight but different structures. Separate detection of raffinose and maltotriose in MALDI MS were presented.