IdenHerb: A strategy for identifying constitutive herbs of herbal products by screening exclusive ions of each herb from large-scale multi-group LC-MS data

Yang Li; Peng Zhan; Shu-Ya Xue; Lin-Han Xiang; Meng-Ge Feng; Li-Qing Wang; Zi-Kang Cheng; Yang Lv; Zhi-Gao Zhao; Wen Ma; Li-Zhi Chen; Guang-Xue Liu; Ming-Ying Shang; Shao-Qing Cai; Feng Xu

doi:10.1016/j.chroma.2025.465716

IdenHerb: A strategy for identifying constitutive herbs of herbal products by screening exclusive ions of each herb from large-scale multi-group LC-MS data

J Chromatogr A. 2025 Jan 22:1743:465716. doi: 10.1016/j.chroma.2025.465716. Online ahead of print.

Authors

Yang Li¹, Peng Zhan¹, Shu-Ya Xue², Lin-Han Xiang¹, Meng-Ge Feng³, Li-Qing Wang¹, Zi-Kang Cheng¹, Yang Lv¹, Zhi-Gao Zhao⁴, Wen Ma¹, Li-Zhi Chen⁵, Guang-Xue Liu¹, Ming-Ying Shang¹, Shao-Qing Cai¹, Feng Xu⁶

Affiliations

¹ Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China.
² School of Computer Science and Technology, Schoow University, Suzhou 215006, China.
³ Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China; Medical College, Tibet University, Lhasa 850002, China.
⁴ Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China; School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
⁵ Shimadzu (China) Co., Ltd., Beijing Branch, Beijing 100020, China.
⁶ Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China; Medical College, Tibet University, Lhasa 850002, China. Electronic address: xufeng76@bjmu.edu.cn.

PMID: 39862541
DOI: 10.1016/j.chroma.2025.465716

Abstract

Identification of constitutive herbs in an herbal product is critical for ensuring its quality and efficacy. However, current identification methods often lack universality, entail long durations, and involve complex procedures. Therefore, there is an urgent need to develop innovative methods for identifying constitutive herbs. This paper aims to propose a more refined, universal, simple, rapid, and eco-friendly method for identifying more constitutive herbs in herbal products, significantly enhancing the precision and efficiency of quality control method of herbal products. Leveraging UHPLC‒Q‒TOF‒MS (ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry) data of herbs and the R language, we devised algorithms to find exclusive ions and diagnostic ions of each herb. An open platform named IdenHerb for identifying constitutive herbs of herbal products was established. Using IdenHerb, exclusive ions of 94 herbs were found, and from these exclusive ions, their diagnostic ions were screened out. These diagnostic ions were successfully applied to identify constitutive herbs of two mixtures of herbal powders and eight Chinese patent medicines. Furthermore, this methodology was evaluated using three commonly encountered adulterants as test cases. After incorporating the LC‒MS data of these adulterants into the comprehensive LC‒MS database of all herbs, this approach demonstrated excellent discriminatory capabilities. Compared to the Chinese Pharmacopoeia (2020 edition), IdenHerb is capable of identifying a greater number of constituent herbs, thereby enhancing the level of quality control for the herbal products. This strategy deserves further research and wide application.

Keywords: Chinese patent medicines; Constitutive herb identification; Exclusive ions; Herbal products; Large-scale data; R language; UHPLC‒Q‒TOF‒MS.