Putative metabolite annotations were derived from the vendor-processed MS-DIAL-aligned feature tables. Annotation information included feature m/z, retention time, adduct information where available, molecular formula, putative compound name, superclass/class/subclass assignment, KEGG Compound ID where available, and vendor annotation scores. No authentic chemical standards were used for structural confirmation; therefore, compound-level labels were treated as putative annotations rather than confirmed metabolite identities. Annotation information was used primarily to summarize interpretable metabolite families and to prioritize features for subsequent validation. Unannotated or insufficiently characterized LC-MS features were retained at the feature level where appropriate.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reversed-phase-c18","Liquid Chromatography MS - positive - reversed-phase-c18"],"chromatography_protocol":["Chromatographic separation was performed using an Agilent 1290 Infinity LC system equipped with a Waters ACQUITY UPLC BEH C18 column (1.7 µm, 2.1 × 100 mm). The column temperature was 40 °C, the flow rate was 0.4 mL/min, the injection volume was 2 µL, and the autosampler temperature was 4 °C. Mobile phase A consisted of water containing 25 mM ammonium acetate and 0.5% formic acid, and mobile phase B was methanol. The gradient program was: 0–0.5 min, 5% B; 0.5–10.0 min, 5–100% B; 10.0–12.0 min, 100% B; 12.0–12.1 min, 100–5% B; and 12.1–16.0 min, 5% B. Samples were analyzed in randomized order, with pooled QC injections distributed throughout the analytical sequence.
"],"publication":["Organ-Resolved Untargeted LC-MS/MS Profiling of Putative Metabolite Families in Aerial Organs of Vitex negundo L. 10.3390/metabo16090633."],"submitter_name":["wang menghu"],"submitter_affiliation":["Bozhou University"],"organism_part":["mixture","leaf","flower","stem"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Fresh tissue (100 mg per sample) was ground in liquid nitrogen and extracted with 400 µL of precooled methanol/acetonitrile/water (2:2:1, v/v/v). Samples were vortexed for 30 s, ultrasonicated for 20 min in a 4 °C water bath, incubated at −20 °C for 30 min, and centrifuged at 14,000 rcf at 4 °C for 20 min. Supernatants were vacuum-dried and reconstituted in 100 µL acetonitrile/water (1:1, v/v), followed by vortexing, centrifugation, and filtration through a 0.22 µm membrane before LC-MS/MS analysis. Pooled quality-control samples were prepared by mixing equal aliquots of all study samples.
"],"organism":["Vitex negundo"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15653"],"author":["wang menghu. Bozhou People's Hospital. shapuofeng@163.com.","meng xiangsong. School of Traditional Chinese Medicine and Health, Bozhou University. No. 2266 Tangwang Avenue, Qiaocheng District, Bozhou, Anhui 236800, China. 2018070005@bzuu.edu.cn.","jiang qianqian."],"data_transformation_protocol":["Vendor-processed aligned feature tables were generated using MS-DIAL version 4.60 for peak detection, deconvolution, retention-time correction, peak alignment, peak-area extraction, and annotation-related processing; ProteoWizard 3.0.6428 was also listed in the processing information. Reported MS-DIAL parameters included an MS1 tolerance of 0.01, MS2 tolerance of 0.025, minimum peak height of 800, minimum peak width of 3, and alignment retention-time tolerance of 0.15. Pooled-QC RSD was recalculated from QC-1, QC-2, and QC-3. Features were retained when detected in at least two of three samples in one or more organ groups and when pooled-QC RSD was ≤30%. Retained intensities were sample-wise median-normalized and log2(x + 1)-transformed for downstream analyses.
"],"study_factor":["Organ"],"submitter_email":["shapuofeng@163.com"],"sample_collection_protocol":["Fresh flower, stem, and leaf tissues of Vitex negundo L. were collected on 14 July 2024 in Bozhou, Anhui Province, China (33.844457° N, 115.768112° E). Plant material was taxonomically authenticated by Xiangsong Meng at Bozhou University, and voucher material (BZXY-20240714-01) was deposited at Bozhou University. Flower, stem, and leaf tissues were collected from the same three individual plants, forming three paired biological blocks. H, J, and Y denote flower, stem, and leaf tissues, respectively; samples sharing the terminal numeral 1–3 originated from the same individual plant. Approximately 1 cm stem segments were collected from the middle portion of second-year stems immediately below the current-year tender shoots.
"],"omics_type":["Metabolomics"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","pooled quality control sample","Metabolomics","untargeted analysis","Agilent 1290 Infinity HPLC","leaf","Agilent 1290 Infinity LC","experimental sample","untargeted metabolite profiling","flower","tandem mass spectrometry","mixture","Vitex negundo","AB SCIEX TripleTOF 6600","stem"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","pooled quality control sample","Metabolomics","untargeted analysis","leaf","Agilent 1290 Infinity HPLC","Agilent 1290 Infinity LC","experimental sample","untargeted metabolite profiling","flower","tandem mass spectrometry","mixture","Vitex negundo","AB SCIEX TripleTOF 6600","stem"],"mass_spectrometry_protocol":["Mass-spectrometric acquisition was performed on an AB SCIEX TripleTOF 6600 instrument using electrospray ionization in positive and negative modes. Source parameters were Gas1 = 60, Gas2 = 60, curtain gas = 30, and source temperature = 600 °C. Ion spray voltage floating was +5500 V in positive mode and −5500 V in negative mode. The TOF-MS scan range was m/z 60–1000 and the product-ion scan range was m/z 25–1000. Information-dependent acquisition was performed in high-sensitivity mode using a declustering potential of ±60 V, collision energy of 35 ± 15 eV, isotope exclusion within 4 Da, and ten candidate ions per acquisition cycle.
"],"metabolite_name":["Phenylpyruvic acid","4-Methoxybenzoic acid","Naringenin","Phenylacetic acid","Kaempferide","Methylsuccinic acid","3,4-Dihydroxybenzoic acid","Palmitic acid","Orsellinic acid","Carnosol","4-Hydroxycinnamic acid","Isokaempferide","Homoeriodictyol","Rhamnetin","Pyridoxal","Tetracosanoic acid","Nervonic acid","4-Hydroxybenzoic acid","Phenylbutazone","Catechol","Hispidulin","Violanone","3-O-Methylquercetin","Sebacic acid","Abietic acid","Epoprostenol","Phenol","D-Malate","Isobavachalcone","Melezitose","4-Vinylphenol","Cianidanol","Neochlorogenic acid","4-Hydroxybenzaldehyde","Glutamic acid","omega-Hydroxyemodin","Osajin","Lactulose","Cinnamic acid","alpha D-Galactose","Umbelliferone","Citrinin","4-Hydroxy-3-methoxycinnamaldehyde","4-Nitrophenol","Pinocembrin","Apigenin","Oleic acid","Mannitol","Luteolin","Pentadecanoic acid","Secoisolariciresinol","Eriodictyol","Salicylic acid","Aspirin","Morin","Phenylalanine","Dodecanedioic acid","Kaempferol","Tryptophan","Glycitein","3-O-Feruloylquinic acid","Quinic acid","Asparagine","Diosmetin-7-O-rutinoside","Mycophenolic acid","Dibutyl phthalate","Galangin","4-Hydroxyphenyl acetate","Quillaic acid","Theobromine","Cosmosiin","Shikimic acid","Diosmetin","2-Amino-3-methoxybenzoic acid","Maleic acid","Vanillic acid","Stachyose","Stearic acid","Chrysosplenetin","Gluconic acid","Hexadecanedioic acid","Galactaric acid","Esculetin","Erythromycin","L-Malic acid","Wedelolactone","Isorhamnetin","Cirsimaritin","Irbesartan","Myristic acid","4-Nitrocatechol","Uridine","Chenodeoxycholic acid","gamma-Linolenic acid","D-Glucose","Leucanthoside","Leucine","Oxazepam","Raffinose","Docosanoic acid","(S)-2-Hydroxy-2-methylsuccinic acid","9,10-Epoxystearic acid","Thiopental","Aspartic acid","Adenine","Chlorogenic acid","Threonic acid","3-Hydroxypropionic acid","Rutin","Isoquercitrin","Linoleic acid","2,3-Dihydroxybenzoic acid","Methylglyoxal","Salicyl alcohol","Stenophylline A","Linolenic acid","Chrysin","Eupatilin","Santin","Vanillin","L-(-)-3-Phenyllactic acid","3-Hydroxyphenylacetic acid","Glutamine"],"additional_accession":[]},"is_claimable":false,"name":"Organ-Resolved Untargeted LC-MS/MS Profiling of Putative Metabolite Families in Aerial Organs of Vitex negundo L","description":"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–tandem 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 ≤ 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−Hochberg 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 < 0.05 and |mean paired log2 difference| ≥ 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.
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