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Detecting PTM sites in proteome scale is one of the key steps to in-depth understanding their regulation mechanisms. In this study, we presented an integrated method based on eXtreme Gradient Boosting (XGBoost), called iRice-MS, to identify 2-hydroxyisobutyrylation, crotonylation, malonylation, ubiquitination, succinylation and acetylation in rice. For each PTM-specific model, we adopted eight feature encoding schemes, including sequence-based features, physicochemical property-based features and spatial mapping information-based features. The optimal feature set was identified from each encoding, and their respective models were established. Extensive experimental results show that iRice-MS always display excellent performance on 5-fold cross-validation and independent dataset test. In addition, our novel approach provides the superiority to other existing tools in terms of AUC value. Based on the proposed model, a web server named iRice-MS was established and is freely accessible at http:\/\/lin-group.cn\/server\/iRice-MS.<\/jats:p>","DOI":"10.1093\/bib\/bbab486","type":"journal-article","created":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T19:15:35Z","timestamp":1635275735000},"source":"Crossref","is-referenced-by-count":28,"title":["iRice-MS: An integrated XGBoost model for detecting multitype post-translational modification sites in rice"],"prefix":"10.1093","volume":"23","author":[{"given":"Hao","family":"Lv","sequence":"first","affiliation":[{"name":"Center for Informational Biology at University of Electronic Science and Technology of China, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Shu","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Informational Biology at University of Electronic Science and Technology of China, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3068-8849","authenticated-orcid":false,"given":"Shi-Shi","family":"Yuan","sequence":"additional","affiliation":[{"name":"Center for Informational Biology at University of Electronic Science and Technology of China, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Jie","family":"Sun","sequence":"additional","affiliation":[{"name":"Center for Informational Biology at University of Electronic Science and Technology of China, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fu-Ying","family":"Dao","sequence":"additional","affiliation":[{"name":"Center for Informational Biology at University of Electronic 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