摘要Natural products(NPs)have long held a significant position in various fields such as medi-cine,food,agriculture,and materials.The chemical space covered by NPs is extensive but of-ten underexplored.Therefore,high-throughput and efficient methodologies for the annota-tion and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the re-leased annotation methodologies,based on a variety of informatics tools,continuously im-prove the ability to annotate the structure and properties of compounds.This review exam-ines the current mainstream databases and annotation methodologies,focusing on their ad-vantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities.