The annotation was performed using the MetaboAnnotation R package. Candidate compounds were compiled from an internal database containing more than 500 metabolites from different chemical classes and the theoretical m/z values of expected adducts were calculated. Feature annotation was achieved by matching theoretical database ions with detected features from the processed datasets using an m/z tolerance of 0.01 Da and a rt tolerance of 0.5 min, taking into account the ionization mode. Rt used for matching corresponded to those previously obtained in the TargetLynx-based approach, together with those of standards analyzed under the same conditions. Annotation levels were assigned according to Sumner et al. (2007)
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Analysis was performed on a Waters Acquity UPLC controlled by MassLynx 4.1, with a reversed phase (RP) an ACQUITY UPLC 1.8 µm 2.1 x 100 mm HSS T3 column (Waters, Manchester, UK) at 30 °C was eluted with a gradient program starting from 100% A (H2O, 0.1 % HCOOH) from 0 till 6 min and then increasing linearly over 56 min to 100 % B (CH3OH, 0.1% HCOOH) where it was held isocratic until 60 min, with a 0.3 ml/min flow rate. The injection volume was 5 µL and the samples were kept at 4 °C throughout the analysis.
"],"publication":["A Metabolome Atlas of Grape Biodiversity. 10.1021/acs.jafc.6c04648."],"submitter_name":["Panagiotis Arapitsas"],"submitter_affiliation":["Fondazione Edmund Mach"],"organism_part":["blank","reference compound","Grape"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Sample homogenization was performed at the end of the 4-year sampling campaign by grinding 200 g of frozen berries under liquid nitrogen with an IKA A11 homogeniser. The powder was then stored in 50 mL falcon flasks at -80 °C.
Briefly, 1 g of each sample powder was weighed into 15 mL amber vials and then 20 µL of the internal standard (IS) (4800 mg/L 4-OH-stilbene, 3000 mg/L gentisic acid, 1200 mg/L indol-propionic acid in CH3OH/H2O (1/1 v/v)), 1.2 mL of H2O:CH3OH (1:2) and 0.8 mL of CHCl3 were added. After vortexing for 1 min, each sample was agitated in an orbital shaker (Grant-Bio Rotator PTR-60) for 15 min at room temperature and then centrifuged at 1000g and 4 °C for 10 min. The upper aqueous methanol phase was collected and filtered through 0.2 µm PTFE filters in 2 mL amber (LC-MS certificated) vials.
The standard mix sample (STDmix) included trans-resveratrol, caffeic acid, ellagic acid, catechin, quercetin, quercetin-3-glucoside, cyanidin-3-galactoside, methyl stearate, 4-aminobutyric acid, glutathione and ursolic acid in methanol/water (70/30).
A pooled sample of six varieties (Sangiovese, Cabernet Sauvignon, Merlot, Riesling, Chardonnay and Gewürztraminer) was selected as the QC sample. Approximately 500 g of berries were sampled from different vine plants and different positions for each vine, and after collecting, all samples were directly frozen and stored at -80 °C.
Data was processed using both a pseudo-targeted and an untargeted approach. For the first, TargetLynx tool from MassLynx 4.1 software was used for the pseudo-targeted integration of the annotated compounds (biomarkers and well-known wine metabolites). The parameters of the integration were set to 0.08 Da for the chromatogram mass window, 0.2 min for the (rt) window, and smoothing iterations of 1 and width of 2. This data was used to interpret the output of the unsupervised analyses of the data processed with the untargeted approach.
For the processing following an untargeted approach, raw LC-MS data files were converted to the open mzML format using the MSCconvert tool of ProteoWizard. All subsequent data processing was performed in R using the “xcms” package.24 Positive and negative ionization modes were processed separately. Spectra were filtered to retain only those acquired within the first 47 minutes of the chromatographic runs. Peak detection was carried out using the centWave algorithm with the following parameters: ppm = 20; peak width = 6–48 s; signal-to-noise threshold = 5; prefilter = c(5, 10); noise = 0; mzdiff = 0.001; integrate = 2. Detected chromatographic peaks were subsequently refined using the “refineChromPeaks” function to merge adjacent peaks (expandRt = 9 s; expandMz = 0.001; minProp = 0.75). Rt correction was performed using the “adjustRtime” function with the peak group method. Alignment was based on QC samples, and the following parameters were applied: minFraction = 1; span = 0.4, subsetAdjust = 'average'. Chromatographic peaks were grouped across samples using the peak density method, with sample groups defined by grape variety. Grouping parameters were: minFraction = 0.75; binSize = 0.02; bandwidth (bw) = 30. Finally, missing peak intensities were filled in using the “fillChromPeaks” function with the default settings from “ChromPeakAreaParam”, generating the final feature intensity matrix for downstream statistical analysis.
"],"study_factor":["Accession","Harvest","Variety"],"submitter_email":["panagiotis.arapitsas@fmach.it"],"sample_collection_protocol":["All the accessions were part of the ampelographic collection of the Fondazione Edmund Mach (international code ITA362). The grapevine panel was selected to represent the six major genetic clusters based on population structure analyses of SSR data. In that study, at K = 5, cultivated V. vinifera ssp. sativa accessions are partitioned into three subpopulations: S1, comprising Mediterranean wine and table grapes; S2, including muscat-flavored wine and table grapes; and S3, encompassing wine cultivars from Central Europe. A distinct group corresponds to V. vinifera ssp. sylvestris (VS), which also includes sativa cultivars showing sylvestris-related ancestry. The remaining groups include non-vinifera (Rs) and admixed accessions (ADM), characterized by the absence of a predominant cluster membership. The panel also included specific hybrids between American species and V. vinifera (Hybrid F1), along with additions relevant cultivars (UNK). The sampling design was intended to ensure representation of these genetic groups focusing primarily on V. vinifera.
All grape samples included in the study were collected from vines cultivated using a standardized system, with Guyot trellising, in vineyards with rows N-S oriented. Healthy grapes were sampled in 2007 (103 varieties), 2008 (120 varieties), 2009 (118 varieties), and 2010 (121 varieties) at the technological maturity (18° Brix) .
"],"omics_type":["Metabolomics"],"study_design":["pooled quality control sample","Metabolomics","Vitis riparia x Vitis berlandieri","blank","Vitis californica","untargeted analysis","Waters ACQUITY UPLC system","Vitis vinifera","reference compound","(Vitis vinifera x Vitis berlandieri) x Vitis berlandieri","UMAP","Vitis x champinii","Vitis cinerea","terpene","grape","reference compound mix","experimental sample","Vitis labrusca x Vitis vinifera","Phenotyping","XCMS","solvent","experimental blank","vitis","Vitis riparia","Waters SYNAPT G1 HDMS System"],"curator_keywords":["pooled quality control sample","Metabolomics","Vitis riparia x Vitis berlandieri","blank","Vitis californica","untargeted analysis","Waters ACQUITY UPLC system","Vitis vinifera","reference compound","(Vitis vinifera x Vitis berlandieri) x Vitis berlandieri","UMAP","Vitis x champinii","Vitis cinerea","terpene","grape","reference compound mix","experimental sample","Vitis labrusca x Vitis vinifera","Phenotyping","XCMS","solvent","experimental blank","vitis","Vitis riparia","Waters SYNAPT G1 HDMS System"],"mass_spectrometry_protocol":["Mass spectrometric data were collected by different runs in positive and negative ESI mode over a mass range of 50 to 3000 amu with scan duration of 0.3 s in centroid mode and in low and high energy. The transfer collision energy and trap collision energy were set at 6 V and 4 V for the low and 30 V and 6 V for high energy acquisition respectively. The source parameters were set as follows: capillary 3 kV for positive scan and 2.5 kV for negative scan, sampling cone 25 V, extraction cone 3 V, source temperature 150uC, desolvation temperature 500uC, desolvation gas flow 1000 L/h and nebulizer gas 50 L/h. External calibration of the instrument was performed at the beginning of each batch of analysis by direct infusion of a sodium formate solution (10% formic acid/0.1 M NaOH/Acetonitrile at a ratio of 1/1/8) by controlling the mass accuracy from 40 to 2000 m/z (less than 5 ppm) and mass resolution (over 14000 FWHM). LockMass calibration was applied using a solution of leucine enkephaline (0.5 mg/L, m/z 556.2771 for positive and 554.2620 for negative ion mode) at 0.1 mL/min.
"],"metabolite_name":["kaempferol 3-O-β-D-glucoside","glucogallin","myricetin 3-glucuronide","phenylalanine","gallocatechin","procyanidin B4","procyanidin B3","quercetin 3-glucuronide","procyanidin B2","gallic acid","isorhamnetin 3-glucoside","quercetin O-glucoside","kaempferol 3-O-glucuronide","myricetin","procyanidin B1","afzelechin","catechin","epicatechin","quercetin","myricetin 3-glucoside","epigallocatechin"],"additional_accession":[]},"is_claimable":false,"name":"A Metabolome Atlas of Grape Biodiversity","description":"Grapevine (Vitis spp.) is one of the world’s most economically, culturally, and biologically important fruit crops, with remarkable diversity spanning thousands of V. vinifera cultivars together with rootstocks and wild relatives. Yet grapevine biodiversity has never been systematically explored at the metabolome scale, despite its importance for chemotaxonomy, breeding, and sustainable viticulture. Here, we present the Grape Metabolome (GM) project, the first systematic LC–MS survey of grapevine biodiversity, comprising 462 samples from 126 accessions collected across four vintages. Advanced and well-established chemometric tools resolved the major grape chemotypes together with finer cultivar-related substructure, while annotation-guided interpretation linked this organization to distinctive patterns in anthocyanins, flavonols, aroma-related compounds, and tannin-associated phenolics. This dataset provides a reference framework for chemotaxonomy, breeding, authenticity, and precision enology.","dates":{"publication":"2026-08-25","submission":"2026-04-25"},"accession":"MTBLS14377","cross_references":{"MetaboLights":["MTBLC31463","MTBLC189578","MTBLC31985","MTBLC74793","MTBLC31799","MTBLC31967","MTBLC75030","MTBLC75689","MTBLC183112","MTBLC192448","MTBLC180830","MTBLC75693","MTBLC172829","MTBLC18186","MTBLC7916","MTBLC8198","MTBLC4775","MTBLC30769","MTBLC27897","MTBLC189437","MTBLC33992","MTBLC90","MTBLC31018","MTBLC42255","MTBLC75633","MTBLC27589","MTBLC75630","MTBLC75632","MTBLC18152","MTBLC168023","MTBLC166633","MTBLC16243","MTBLC64621","MTBLC131700","MTBLC30200","MTBLC75721","MTBLC75750","MTBLC2507","MTBLC15834","MTBLC30778","MTBLC28044"],"ChEBI":["CHEBI:31463","CHEBI:189578","CHEBI:31985","CHEBI:74793","CHEBI:31799","CHEBI:31967","CHEBI:75030","CHEBI:75689","CHEBI:183112","CHEBI:192448","CHEBI:180830","CHEBI:75693","CHEBI:172829","CHEBI:18186","CHEBI:7916","CHEBI:8198","CHEBI:4775","CHEBI:30769","CHEBI:27897","CHEBI:189437","CHEBI:33992","CHEBI:90","CHEBI:31018","CHEBI:42255","CHEBI:75633","CHEBI:27589","CHEBI:75630","CHEBI:75632","CHEBI:18152","CHEBI:168023","CHEBI:166633","CHEBI:16243","CHEBI:64621","CHEBI:131700","CHEBI:30200","CHEBI:75721","CHEBI:75750","CHEBI:2507","CHEBI:15834","CHEBI:30778","CHEBI:28044"]}}