Extraction strategy drives MALDI fingerprinting and class separability in rice seed storage proteins

Rice is a staple cereal worldwide, with its proteins essential for nutrition and technology. This study examined three extraction methods—direct, modified sequential, and sequential—on the protein composition of albumin, globulin, glutelin, and prolamin in Arborio, Carnaroli, and Roma rice varieties. Utilizing SDS-PAGE, MALDI-TOF mass spectrometry, and multivariate statistical techniques (PCA and PERMANOVA), the results showed that sequential extraction was the most effective and reproducible method, producing distinct protein profiles. The extraction method significantly affected the protein profile, particularly in the alcohol- and salt-soluble fractions. Moreover, significant differences among varieties were observed in the albumin fraction. This study emphasizes the need for standardized methods in rice proteomic analysis and suggests that albumin profiling could serve as an effective tool for quality control and traceability of rice varieties, given its sensitivity to varietal differences. • A comparative study on the rice seeds protein fractions using three different extraction methods. • Sequential extraction yields the most consistent and informative protein profiles. • Albumins exhibit their potential for authenticating rice varieties. • The glutelins and prolamins profiles are affected by the extraction method. • MALDI fingerprinting is an efficient and quick technique for profiling rice proteins.