Example Studies
The following are examples of well annotated studies which employ different technology or belong to different disciplines.
| Study ID | Study title | Authors | Keyword (Ontology) | Measurement type | Organism (Ontology) | Organism part (Ontology) | Factors (Ontology) | Sample Type | Technique / Acquisition Mode | Chromatography | Mass spectrometry | Metabolite Annotation | Data Files | Publication |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MTBLS3563 | Impact of in vitro hormone treatments on the bibenzyl production of Radula complanata (Untargeted metabolomics) | Steffen Neumann; Kristian Peters; Kaitlyn Blatt-Janmaat | Mosses; lichens; liverworts (organism) (SNOMED); Plant Metabolomics (MTBLS); plant hormone (CHEBI); untargeted metabolites (MTBLS); ultra-performance liquid chromatography-mass spectrometry (CHMO); tandem mass spectrometry (CHMO); bibenzyl | Untargeted Metabolomics | Radula complanata (NCBITaxon) | Whole plant (BTO) | Phytohormone treatment: treatment (EFO); Phytohormone concentration: concentration (CHMO) | Experimental Samples (CHMO) | LC-MS/MS; DDA mode; reverse-phase; POS; NEG | Bruker Elite HPLC system; NUCLEODUR X18 C18 Gravity-SB (1.8 µm, 2 mm x 100 mm; Macherey-Nagel) column; 35 °C column oven temperature; binary solvent gradient (0.1% F A: solvent A, MeCN: solvent B); 0.5 mL/min flow rate | Bruker timsTOF Pro; ESI; Q-TOF; scan mass range: 20-1300 m/z | ChEBI ID; Chemical Formula; SMILES; InChI; Metabolite ID; m/z; Modifications; Charge; RT | .d; .mzML | DOI: https://doi.org/10.1139/cjb-2022-0048; DOI: https://doi.org/10.1007/s11306-023-01979-y |
| MTBLS4381 | Metabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial A - seaweed-dose response) | Varsha Kale; Jacob Rasmussen; Sandy Rogers | HoloFood; Gut Content; Intestinal Flora (NCIT); untargeted metabolites(MTBLS); nanoflow liquid chromatography-tandem mass spectrometry (CHMO); intestine (BTO); Atlantic salmon; BioSamples (NCIT); Host-Microbe Interactions | Untargeted Metabolomics | Salmo salar (NCBITaxon); blank | Intestinal content (NCIT); solvent (CHEBI) | Animal ID: Animal ID; Treatment: treatment (EFO); Sampling time: timepoint (EFO); Tank code: block (EFO) | Experimental Samples (CHMO); blanks, pooled quality control samples (MTBLS) | LC-MS/MS; DDA mode; reverse-phase; POS | Thermo Scientific Dionex UltiMate 3000 RSLCnano System; Acclaim PepMap RSLC C18 (3 µm, 0.075 mm x 150 mm; Thermo Scientific) column; 40 °C column oven temperature; solvent gradient (0.1% FA in 98% H2O: 2% MeCN: solvent A, 0.1% FA in 2% H2O: 98% MeCN: solvent B); 0.3 mL/min flow rate | Thermo Scientific Q Exactive HF; nanoESI; Orbitrap; scan mass range: 200-1000 m/z | ChEBI ID; Chemical Formula; SMILES; InChI; Metabolite ID; m/z; Modifications; Charge; RT; taxid; species; search_engine; feat_ID; Compound_Source and other 12 extra Compound related classification features; Quantification_values | .raw; .mzML | NIAID Data Ecosystem: https://data.niaid.nih.gov/resources?id=mtbls4381 |
| MTBLS718 | Antiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19 | MRC-NIHR National Phenome Centre | untargeted metabolites (MTBLS); COVID-19 (DOID); CMPK2 (OGG); SPATS2L (OGG); IFI27 (OGG); RSAD2 (OGG); ultra-performance liquid chromatography-mass spectrometry(CHMO); tandem mass spectrometry(CHMO); biomarker (CHEBI); Lipidomics (NCIT) | Untargeted Metabolomics; Lipidomics | Homo sapiens (NCBITaxon) | Blood serum(BTO) | Cohort: cohort (EFO); Gender: Gender (NCIT); Age: age (EFO); Condition: Condition (NCIT); ITU admission (COVID only): Patient Admission (OMIT); Mortality (COVID only): mortality (EFO); Sample Collection: Date (NCIT); Delay to freezer storage: timepoint (EFO); Creatinine Concentration: concentration (CHMO); Sample Dilution: Sample Dilution (NCIT); CPMK2: Sequence Read Count (NCIT); SPATS2L: Sequence Read Count (NCIT); IFI27: Sequence Read Count (NCIT); RSAD2 (viperin): Sequence Read Count (NCIT); unnamed: Sequence Read Count (NCIT) | Experimental Samples (CHMO), pooled quality control samples (MTBLS) | LC-MS/MS; reverse-phase; HILIC; POS; NEG | Waters ACQUITY UPLC system; Waters 2777C Sample Manager; ACQUITY UPLC BEH HILIC (1.7 µm, 2.1 mm x 150 mm; Waters); ACQUITY UPLC BEH C8 (1.7 µm, 2.1 mm x 100 mm; Waters) column; 40 °C (HILIC) and 55 °C (RP) column oven temperature; solvent gradient (0.1% FA in MeCN: solvent A, 0.1% FA and 20 mM ammonium formate in H2O: solvent B); 0.6 mL/min - 1 mL/min flow rate (HILIC); temperature; solvent gradient (H2O:isopropanol:MeCN (2:1:1, v/v/v), 5 mM ammonium acetate, 0.05% acetic acid, 20 µM phosphoric acid: solvent A,isopropanol:acetonitrile (1:1, v/v), 5 mM ammonium acetate, 0.05% acetic acid: solvent B); 0.6 mL/min - 1 mL/min flow rate (RP- Lipidomics) | Waters Xevo G2-S QTof ESI; Q-TOF; scan mass range: 50-1200 m/z (HILIC) and 50-2000 m/z (RP-Lipidomics) | Metabolite ID; m/z values; Modifications; Charge; RT; reliability; Quantification_values | .raw.zip; .mzML | DOI: https://doi.org/10.1016/j.medj.2022.01.009 |
| MTBLS1820 | Extracellular reef metabolites across the protected Jardines de la Reina, Cuba reef-system | Laura Weber | Coral reef sea water (ENVO); targeted metabolites (MTBLS); untargeted metabolites (MTBLS); Dissolved Organic Matter (MESH); ultra-performance liquid chromatography-mass spectrometry (CHMO); Marine Metabolomics; coral metabolite (CHEBI); tandem mass spectrometry (CHMO) | Untargeted Metabolomics; Targeted Metabolomics | Sea water (ENVO) | Exometabolome (MTBLS) | Sea water location: Location (NCIT); Depth: Depth (NCIT); Replicate: technical replicate (EFO); Profiling: metabolite profiling assay (OBI) | Experimental Samples (CHMO); pooled quality control samples (MTBLS) | LC-MS/MS; reverse-phase; NEG; Alternating | Thermo Scientific Vanquish UHPLC System (Untargeted); Thermo Scientific Accela 1250 Pump and Thermo Scientific Accela Open Autosampler (Targeted); ACQUITY UPLC HSS T3 (1.8 µm, 2.1 mm x 100 mm; Waters); ACQUITY UPLC HSS T3 VanGuard Pre-column (1.8 µm, 2.1 mm x 5 mm; Waters); 40 °C column oven temperature; (0.1% FA in H2O: solvent A, 0.1% FA in MeCN: solvent B); 0.5 mL/min flow rate (Untargeted and Targeted) | Thermo Scientific Orbitrap Fusion Lumos Tribrid; ESI; Orbitrap; scan mass range: 100-1000 m/z (Untargeted); Thermo Scientific TSQ Vantage; ESI; Triple Quadrupole; scan mass range: SRM (Targeted) | m/z; RT; Quantification_values | .raw; .mzML | DOI: https://doi.org/10.3389/fmars.2020.582161 |
| MTBLS2289 | Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth | Fidel Lozano-Elena | untargeted metabolites (MTBLS); drought tolerance (TO); brassinosteroid (CHEBI); Genetic (NCIT); Growth (NCIT); gas chromatography time-of-flight mass spectrometry (CHMO); BRL3 (Arabidopsis thaliana) | Untargeted Metabolomics | Arabidopsis thaliana (NCBITaxon); blank | root (BTO); shoot (BTO) | Genotype: genotype (EFO); Timepoint: timepoint (EFO); Drought stress: treatment (EFO); Replicate: replicate (EFO); Sample weight: Weight (NCIT) | Experimental Samples (CHMO); blanks | GC-MS | Agilent 6890N GC; Agilent CTC Analytics Combi PAL autosampler; DB-35 GC (0.25 µm, 0.32 mm x 30 m; Agilent Technologies) column | LECO Pegasus III; EI; TOF; scan mass range: 70-600 m/z | ChEBI ID; Chemical Formula; SMILES; InChI; Metabolite ID;taxid; species; Quantification_values | .peg; .cdf | DOI: https://doi.org/10.1038/s41467-018-06861-3 |