In order to supply potato (Solanum tuberosum L) tubers for the processed food industry throughout the year, suppliers should provide consistent quality potatoes even after long-term storage. Despite being one of the most important foods, there is no simple way to control tuber quality and, in particular, controlling sprouting. Chemical suppression such as chlorpropham is used to inhibit sprouting, however, the regulatory status of such chemical inhibition differs in each country. Gas chromatography mass spectrometry-based metabolomics was applied to identify the applicable biomarkers for prediction of potato sprouting during long-term storage. Sprouting was measured in chipping potatoes, and these were also subjected to metabolite profiling to develop a predictive model. The model was based on projections to latent structures (PLS) regression calculated from a metabolome data set obtained before storage and was consistent with actual measured sprouting values. Sucrose, phosphate, and amino acids were selected as valid contributing biomarkers for prediction in a validation field experiment. These biomarkers will contribute to the development of a successful novel method for prediction and control of potato tuber quality during long-term storage. (C) 2019, The Society for Biotechnology, Japan. All rights reserved.