{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T10:17:25Z","timestamp":1788171445072,"version":"build-2803163510"},"reference-count":39,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010814","name":"Anhui Provincial Outstanding Young Teacher Cultivation Project","doi-asserted-by":"publisher","award":["YQYB2024085"],"award-info":[{"award-number":["YQYB2024085"]}],"id":[{"id":"10.13039\/501100010814","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010814","name":"Anhui Provincial Outstanding Young Teacher Cultivation Project","doi-asserted-by":"publisher","award":["YQYB2023064"],"award-info":[{"award-number":["YQYB2023064"]}],"id":[{"id":"10.13039\/501100010814","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010814","name":"Scientific Research Project of the Education Department of Anhui Province","doi-asserted-by":"publisher","award":["2025AHGXZK20162"],"award-info":[{"award-number":["2025AHGXZK20162"]}],"id":[{"id":"10.13039\/501100010814","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010814","name":"Scientific Research Project of the Education Department of Anhui Province","doi-asserted-by":"publisher","award":["2025AHGXZK31301"],"award-info":[{"award-number":["2025AHGXZK31301"]}],"id":[{"id":"10.13039\/501100010814","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010814","name":"Scientific Research Project of the Education Department of Anhui Province","doi-asserted-by":"publisher","award":["2024AH051308"],"award-info":[{"award-number":["2024AH051308"]}],"id":[{"id":"10.13039\/501100010814","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Project of TCM Inheritance and Innovation of Anhui Province","award":["2025CCCX078"],"award-info":[{"award-number":["2025CCCX078"]}]},{"name":"Scientific Research Project of TCM Inheritance and Innovation of Anhui Province","award":["2025CCCX207"],"award-info":[{"award-number":["2025CCCX207"]}]},{"name":"Science and Technology Planning Project of Bozhou","award":["bzzd2025004"],"award-info":[{"award-number":["bzzd2025004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>Background\/Objectives: Vitex negundo L. is a multi-part medicinal and aromatic plant, but organ-resolved chemical information for its aerial organs remains incomplete. This study generated an exploratory paired untargeted liquid chromatography\u2013tandem mass spectrometry (LC-MS\/MS) dataset for flowers, stems, and leaves and prioritized organ-associated putative metabolite families for subsequent validation. Methods: To reduce inter-individual background variation, flower, stem, and leaf tissues were harvested from the same three V. negundo individuals to form n = 3 paired plant blocks. LC-MS\/MS feature data were filtered using pooled quality-control relative standard deviation (QC RSD \u2264 30%), median-normalized and log2-transformed. Principal component analysis (PCA) provided an unsupervised overview, and paired feature-level comparisons were performed using paired t-tests with Benjamini\u2212Hochberg false discovery rate (FDR) correction. Results: A total of 42,125 QC-filtered LC-MS features were retained. PCA showed organ-associated separation among flowers, stems, and leaves. Using FDR &lt; 0.05 and |mean paired log2 difference| \u2265 1, paired screening yielded 13,043, 22,836, and 13,393 FDR-supported LC-MS features for flower vs. stem, flower vs. leaf, and stem vs. leaf comparisons, respectively. Higher-scoring putative annotations suggested organ-associated putative family-level patterns, including flavonoid-related, hydroxycinnamic-acid derivative, phenolamide-related, triterpenoid-related, iridoid-related, and lignan-related signals. Conclusions: This organ-resolved dataset provides a chemical-feature framework for V. negundo aerial organs and putative family-level patterns for future structural confirmation, targeted quantification, bioactivity evaluation, and quality-marker development. Feature counts are not equivalent to unique metabolite counts, and compound labels require validation before being interpreted as confirmed structures.<\/jats:p>","DOI":"10.3390\/metabo16090633","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T09:21:19Z","timestamp":1788168079000},"page":"633","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Organ-Resolved Untargeted LC-MS\/MS Profiling of Putative Metabolite Families in Aerial Organs of Vitex negundo L."],"prefix":"10.3390","volume":"16","author":[{"given":"Menghu","family":"Wang","sequence":"first","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Xinyang","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Xue","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Yafeng","family":"Zuo","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Dong","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Qianqian","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"given":"Xiangsong","family":"Meng","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine and Health, Bozhou University, Bozhou 236800, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"ref_1","first-page":"30","article-title":"A review on Vitex negundo L.\u2014A medicinally important plant","volume":"3","author":"Vishwanathan","year":"2010","journal-title":"Eur. J. Biol. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1002\/ptr.5303","article-title":"Phytochemical and pharmacological profile of Vitex negundo","volume":"29","author":"Zheng","year":"2015","journal-title":"Phytother. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/S0378-8741(03)00159-4","article-title":"Anti-inflammatory and analgesic activities of mature fresh leaves of Vitex negundo","volume":"87","author":"Dharmasiri","year":"2003","journal-title":"J. Ethnopharmacol."},{"key":"ref_4","first-page":"163","article-title":"Antinociceptive activity of Vitex negundo Linn. leaf extract","volume":"49","author":"Gupta","year":"2005","journal-title":"Indian J. Physiol. Pharmacol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1016\/j.foodchem.2005.10.069","article-title":"Antioxidant properties of different fractions of Vitex negundo Linn","volume":"100","author":"Tiwari","year":"2007","journal-title":"Food Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S0378-8741(98)00057-9","article-title":"Screening of 34 Indian medicinal plants for antibacterial properties","volume":"62","author":"Ignacimuthu","year":"1998","journal-title":"J. Ethnopharmacol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.bmcl.2006.09.051","article-title":"New antifungal flavonoid glycoside from Vitex negundo","volume":"17","author":"Sathiamoorthy","year":"2007","journal-title":"Bioorganic Med. Chem. Lett."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jpba.2015.01.049","article-title":"Identification and quantification of phenolic compounds in Vitex negundo L. var. cannabifolia (Siebold et Zucc.) Hand.-Mazz. using liquid chromatography combined with quadrupole time-of-flight and triple quadrupole mass spectrometers","volume":"108","author":"Huang","year":"2015","journal-title":"J. Pharm. Biomed. Anal."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Wu, Q., Zheng, J., Yu, Y., Li, Z., Li, Y., Hu, C., Zhou, Y., and Chen, R. (2024). Analysis of Antioxidant Compounds in Vitex negundo Leaves Using Offline 2D-LC-ECD and LC-MS\/MS. Molecules, 29.","DOI":"10.3390\/molecules29133133"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"106693","DOI":"10.1016\/j.fitote.2025.106693","article-title":"Comparison in chemical constituents and anti-inflammatory and analgesic effects of different medicinal parts from a Vitex negundo L. var. cannabifolia","volume":"185","author":"Zhu","year":"2025","journal-title":"Fitoterapia"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0031-9422(03)00300-5","article-title":"Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective","volume":"64","author":"Wink","year":"2003","journal-title":"Phytochemistry"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2831","DOI":"10.1016\/j.phytochem.2007.09.017","article-title":"From waste products to ecochemicals: Fifty years research of plant secondary metabolism","volume":"68","author":"Hartmann","year":"2007","journal-title":"Phytochemistry"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1146\/annurev-arplant-042110-103814","article-title":"Convergent evolution in plant specialized metabolism","volume":"62","author":"Pichersky","year":"2011","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1126\/science.1217411","article-title":"The rise of chemodiversity in plants","volume":"336","author":"Weng","year":"2012","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.plantsci.2012.07.014","article-title":"Flavonoids as antioxidants in plants: Location and functional significance","volume":"196","author":"Agati","year":"2012","journal-title":"Plant Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/s10311-006-0068-8","article-title":"Significance of flavonoids in plant resistance: A review","volume":"4","author":"Treutter","year":"2006","journal-title":"Environ. Chem. Lett."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/mp\/ssp106","article-title":"Phenylpropanoid biosynthesis","volume":"3","author":"Vogt","year":"2010","journal-title":"Mol. Plant"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e0152","DOI":"10.1199\/tab.0152","article-title":"The phenylpropanoid pathway in Arabidopsis","volume":"9","author":"Fraser","year":"2011","journal-title":"Arab. Book"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1111\/nph.13243","article-title":"Ecology and evolution of floral volatile-mediated information transfer in plants","volume":"206","author":"Schiestl","year":"2015","journal-title":"New Phytol."},{"key":"ref_20","first-page":"3","article-title":"A new concept on quality marker for quality assessment and process control of Chinese medicines","volume":"9","author":"Liu","year":"2017","journal-title":"Chin. Herb. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.apsb.2017.04.012","article-title":"Approaches to establish Q-markers for the quality standards of traditional Chinese medicines","volume":"7","author":"Yang","year":"2017","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1023\/A:1013713905833","article-title":"Metabolomics-the link between genotypes and phenotypes","volume":"48","author":"Fiehn","year":"2002","journal-title":"Plant Mol. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1111\/j.1469-8137.2005.01632.x","article-title":"Plant metabolomics: From holistic hope, to hype, to hot topic","volume":"169","author":"Hall","year":"2006","journal-title":"New Phytol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrm3314","article-title":"Metabolomics: The apogee of the omics trilogy","volume":"13","author":"Patti","year":"2012","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s11306-007-0082-2","article-title":"Proposed minimum reporting standards for chemical analysis","volume":"3","author":"Sumner","year":"2007","journal-title":"Metabolomics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/nprot.2011.335","article-title":"Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry","volume":"6","author":"Dunn","year":"2011","journal-title":"Nat. Protoc."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1007\/s11306-018-1367-3","article-title":"Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies","volume":"14","author":"Broadhurst","year":"2018","journal-title":"Metabolomics"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"van den Berg, R.A., Hoefsloot, H.C.J., Westerhuis, J.A., Smilde, A.K., and van der Werf, M.J. (2006). Centering, scaling, and transformations: Improving the biological information content of metabolomics data. BMC Genomics, 7.","DOI":"10.1186\/1471-2164-7-142"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1021\/ac051437y","article-title":"XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification","volume":"78","author":"Smith","year":"2006","journal-title":"Anal. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1021\/ac202450g","article-title":"CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography\/mass spectrometry data sets","volume":"84","author":"Kuhl","year":"2012","journal-title":"Anal. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nmeth.3393","article-title":"MS-DIAL: Data-independent MS\/MS deconvolution for comprehensive metabolome analysis","volume":"12","author":"Tsugawa","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1038\/s41587-020-0531-2","article-title":"A lipidome atlas in MS-DIAL 4","volume":"38","author":"Tsugawa","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1021\/es5002105","article-title":"Identifying small molecules via high resolution mass spectrometry: Communicating confidence","volume":"48","author":"Schymanski","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Blazenovic, I., Kind, T., Ji, J., and Fiehn, O. (2018). Software tools and approaches for compound identification of LC-MS\/MS data in metabolomics. Metabolites, 8.","DOI":"10.3390\/metabo8020031"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1007\/s11306-014-0656-8","article-title":"Metabolite identification: Are you sure? And how do your peers gauge your confidence?","volume":"10","author":"Creek","year":"2014","journal-title":"Metabolomics"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1146\/annurev.arplant.54.031902.134938","article-title":"Lignin biosynthesis","volume":"54","author":"Boerjan","year":"2003","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1893","DOI":"10.1104\/pp.104.049981","article-title":"Biochemistry of plant volatiles","volume":"135","author":"Dudareva","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nprot.2006.59","article-title":"Gas chromatography mass spectrometry-based metabolite profiling in plants","volume":"1","author":"Lisec","year":"2006","journal-title":"Nat. Protoc."}],"container-title":["Metabolites"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-1989\/16\/9\/633\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T09:42:32Z","timestamp":1788169352000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-1989\/16\/9\/633"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":39,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["metabo16090633"],"URL":"https:\/\/doi.org\/10.3390\/metabo16090633","relation":{},"ISSN":["2218-1989"],"issn-type":[{"value":"2218-1989","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,31]]}}}