Metabolites were identified by comparison to known standards using retention time, parent mass-to-charge value, and at least one fragment mass-to-charge value.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse phase","Liquid Chromatography MS - positive - reverse phase"],"chromatography_protocol":["Liquid chromatography was performed as described [1] on a UHPLC system (Vanquish Binary pump and autosampler) using a reverse phase column (Waters Acquity HSS T3 column (2.1 x 100 mm, 1.8 μm) with a Vanguard pre-column at 40 °C). The mobile phase was (A) 0.1% formic acid in water and (B) 0.1% formic acid in acetonitrile at a flow rate of 0.5 ml/min. The gradient conditions were 0-0.5 min (1% B), 2 min (10% B), 2-5 min (10% B), 7 min (25% B), 7-9 min (25% B), 12.5 min (50% B), 13 min (95% B), 13-14.5 min (95% B). Separate injections of 5 μl each were made for positive and negative ion modes. Samples were randomized before running on the mass spectrometer.
[1] Widner, B., Kido Soule, M. C., Ferrer-González, F., Moran, M. A., & Kujawinski, E. B. (2021). Quantification of amine- and alcohol-containing metabolites in saline samples using pre-extraction benzoyl chloride derivatization and ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC MS/MS). Analytical Chemistry, 93, 4809-4817. doi:10.1021/acs.analchem.0c03769
"],"publication":["Under the sea (ice): Concentration, composition, and bioavailability of dissolved organic carbon. 10.26434/chemrxiv-2025-w0dmz."],"submitter_name":["Krista Longnecker"],"submitter_affiliation":["Woods Hole Oceanographic Institution"],"organism_part":["exometabolome"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Metabolites in the filtrate were derivatized with benzoyl chloride following the protocol detailed in Widner et al. (2021)[1]. Samples were randomized before extractions were done. Triplicate 25 ml vials were processed for each sample. To each 25 ml vial, 750 ul of 8M sodium hydroxide was added, followed by 5ml of working reagent (5% benzoyl chloride in acetone vol:vol). Samples were shaken for 5 min and then acidified with concentrated phosphoric acid to pH 2-3 (375 µl). The acetone was evaporated using a Vacufuge (Eppendorf). Samples were extracted using solid phase extraction Bond Elut PPL cartridges (Agilent, 1 g/6 ml) that were conditioned by rinsing with 1 cartridge volume of methanol, followed by 2 cartridge volumes of acidified MilliQ water (pH 2-3, HCl). Following conditioning, the aqueous phase of each sample was loaded onto each cartridge by gravity and the cartridge was then rinsed with 4 cartridge volumes of acidified MilliQ water. After drying the cartridge under vacuum for five minutes, the samples were eluted with methanol (6 ml). Eluents were dried down in a Vacufuge, reconstituted in 95:5 water:acetonitrile (500 µl). The samples were vortexed and spun at 1000 x g for 15 minutes, after which the supernatant was transferred to an Eppendorf tube. A second aliquot of 500 ul of 95:5 water:acetonitrile was added to the pellet, the sample vortexed, and spun again at 1000 x g for 15 minutes. The supernatant from the second wash was combined with the first wash in the Eppendorf tube. The solution in the Eppendorf tube was spun at 12000 x g for 15 minutes, and then was dried in a Vacufuge. After drying, 100 ul of 95:5 water:acetonitrile with labeled standards was added to the Eppendorf tube, the vial was vortexed, and then spun at 12000 x g for 15 minutes. 80 ul of the supernatant was then transferred to an insert in an LC vial in preparation for mass spectrometry analysis.
[1]Widner, B., Kido Soule, M. C., Ferrer-González, F., Moran, M. A., & Kujawinski, E. B. (2021). Quantification of amine- and alcohol-containing metabolites in saline samples using pre-extraction benzoyl chloride derivatization and ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC MS/MS). Analytical Chemistry, 93, 4809-4817. doi:10.1021/acs.analchem.0c03769
"],"organism":["sea water"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS12381"],"author":["Krista Longnecker. Woods Hole Oceanographic Institution. 266 Woods Hole Road; MS #4; Woods Hole, MA, 02543; United States of America. klongnecker@whoi.edu. 1-508-289-2824."],"data_transformation_protocol":["Sample and standard peak areas were integrated on the RAW XCalibur files using Skyline[1][2], and post-Skyline processing was done in MATLAB. Standard curves were calculated using at least 5 standards, where standard curves were prepared in aged deep sea water ranged from 0.5 to 500 ng/ml. Standard curve R squared values were required to be greater than 0.92 for metabolite quantification. Concentrations were corrected for matrix effects using the analytical recovery of a standard mix spiked into each sample. Because of this correction, we are reporting 'adjusted concentration' for metabolites. The units are pM.
Ref:
[1] Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev. 2020 May;39(3):229-244. doi:10.1002/mas.21540. PMID:28691345
[2] Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN. Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin. Clin Chem. 2018 Feb;64(2):408-410. doi:10.1373/clinchem.2017.282293. PMID:29203474
"],"study_factor":["Latitude","Longitude","Date"],"submitter_email":["klongnecker@whoi.edu"],"sample_collection_protocol":["All sampling took place in Stefansson Sound, Alaska when the offshore area was covered by sea ice. Seawater from under sea ice was collected from late March to May 2023. Sampling dates are given in the metadata as (year-month-day) yyyy-m-d. Sampling locations were accessed daily by snowmachines. Trained wildlife-detection dogs were used to locate holes in sea ice excavated and maintained by ringed seals or holes were drilled at pre-determined locations. Seawater was collected using a 2 L polycarbonate bottles mounted to a pole designed to collect water at a fixed depth of 1 m below the surface of the sea ice. Seawater samples were returned to land-based laboratory where sampling processing began within eight hours of sample collection. Seawater was filtered with 0.2 µM µM Omnipore filters (Whatman) in 25 ml aliquots into combusted 40 ml glass vials and stored frozen at -20 C until sample processing.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","sea water","Thermo Scientific Orbitrap Fusion Lumos Tribrid","untargeted analysis","bioavailability","seawater","sea ice","exometabolome","dissolved organic carbon","experimental sample"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","sea water","Thermo Scientific Orbitrap Fusion Lumos Tribrid","untargeted analysis","bioavailability","seawater","sea ice","exometabolome","dissolved organic carbon","experimental sample"],"mass_spectrometry_protocol":["Samples were analyzed as described [1] in both negative and positive ion mode on an ultrahigh resolution tribrid mass spectrometer, the Orbitrap Fusion Lumos (Thermo Fisher Scientific) following heated electrospray ionization (H-ESI). The Lumos was operated in full-scan MS mode (175 to 1500 m/z scan range) with data-dependent tandem mass spectrometry, guided by a list of user-defined parent ions with a retention time window for each (full MS/ddMS2 with inclusion list). In this targeted quantitation approach, data is collected in full-scan mode in the Orbitrap analyzer. When any of the parent ions on the inclusion list are detected within the retention time window, MS/MS scans are automatically acquired and then the instrument resumes full-scan operation. All data were collected in profile mode.
[1] Widner, B., Kido Soule, M. C., Ferrer-González, F., Moran, M. A., & Kujawinski, E. B. (2021). Quantification of amine- and alcohol-containing metabolites in saline samples using pre-extraction benzoyl chloride derivatization and ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC MS/MS). Analytical Chemistry, 93, 4809-4817. doi:10.1021/acs.analchem.0c03769
"],"metabolite_name":["inosine","2,3-dihydroxypropane-1-sulfonate","taurocholic acid","5-hydroxy-L-tryptophan","cysteine","kynurenine","isoleucine","arginine","glycine","putrescine","homoserine","leucine","taurine","malic acid","inosine 5'-monophosphate","lysine","proline","2' deoxyuridine","n-acetyl glucosamine","syringic acid","phosphoserine","hydroxyproline","s-(1-2-dicarboxyethyl)glutathione","pantothenic acid","glutathione","N-acetyl-D-glucosamine 6-phosphate","pantoic acid","asparagine","glutamine","shikimic acid","uridine","cysteate","sn-glycerol 3-phosphate","fructose 6-phosphate","2'-deoxyguanosine","alanine","folic acid","tryptophan","uridine 5'-monophosphate","4-amino-5-aminomethyl-2-methylpyrimidine","adenosine 5'-monophosphate","acetylserine","trehalose","D-glucosamine 6-phosphate","beta-alanine","hexose-6-phosphate","O-phospho-L-homoserine","threonine","adenine","?-aminobutyric acid","valine","xanthosine","histidine","isethionic acid"],"additional_accession":[]},"is_claimable":false,"name":"Composition and consumption of dissolved organic carbon in seawater under sea ice","description":"Polar regions are an under-studied environment within the global ocean, with seawater found under sea ice particularly under-sampled. This project provides concentrations of select dissolved organic carbon compounds found in under-ice seawater sampled between March and May 2023. The dissolved organic compounds were derivatized with benzoyl chloride in order to improve capture of otherwise polar compounds from seawater. The resulting data set provides into the dissolved organic compounds present in the region, which will be linked to other biological processes in the region.
","dates":{"publication":"2026-07-02","submission":"2025-04-08"},"accession":"MTBLS12381","cross_references":{"MetaboLights":["MTBLC15372","MTBLC17256","MTBLC15698","MTBLC28931","MTBLC39874","MTBLC30753","MTBLC17319","MTBLC17957","MTBLC16892","MTBLC21615","MTBLC16680","MTBLC16335","MTBLC15682","MTBLC22660","MTBLC17126","MTBLC28681","MTBLC84373","MTBLC15573","MTBLC18211","MTBLC16283","MTBLC17562","MTBLC16040","MTBLC16691","MTBLC27592","MTBLC47977","MTBLC16015","MTBLC27744","MTBLC16750","MTBLC16255","MTBLC156381","MTBLC16488","MTBLC16811","MTBLC7027","MTBLC17268","MTBLC17697","MTBLC15729","MTBLC28044","MTBLC16709","MTBLC17822","MTBLC16610","MTBLC16765","MTBLC17895","MTBLC17172","MTBLC16450","MTBLC16027","MTBLC17202","MTBLC16695","MTBLC17780","MTBLC77138","MTBLC16865","MTBLC59640","MTBLC142440","MTBLC16708","MTBLC16977","MTBLC44549","MTBLC29016","MTBLC17196","MTBLC16958","MTBLC17285","MTBLC15356","MTBLC27470","MTBLC15946","MTBLC47987","MTBLC4170","MTBLC28300","MTBLC16856","MTBLC15428","MTBLC15971","MTBLC15699","MTBLC18095","MTBLC17596","MTBLC1157","MTBLC25017","MTBLC16946","MTBLC24898","MTBLC18019","MTBLC6650","MTBLC15784","MTBLC17981","MTBLC15961","MTBLC15811","MTBLC14737","MTBLC7916","MTBLC26271","MTBLC17148","MTBLC16119","MTBLC15978","MTBLC68329","MTBLC15891","MTBLC36276","MTBLC16857","MTBLC16551","MTBLC27897","MTBLC16704","MTBLC16414","MTBLC18107"],"ChEBI":["CHEBI:15372","CHEBI:17256","CHEBI:15698","CHEBI:28931","CHEBI:39874","CHEBI:30753","CHEBI:17319","CHEBI:17957","CHEBI:16892","CHEBI:21615","CHEBI:16680","CHEBI:16335","CHEBI:15682","CHEBI:22660","CHEBI:17126","CHEBI:28681","CHEBI:84373","CHEBI:15573","CHEBI:18211","CHEBI:16283","CHEBI:17562","CHEBI:16040","CHEBI:16691","CHEBI:27592","CHEBI:47977","CHEBI:16015","CHEBI:27744","CHEBI:16750","CHEBI:16255","CHEBI:156381","CHEBI:16488","CHEBI:16811","CHEBI:7027","CHEBI:17268","CHEBI:17697","CHEBI:15729","CHEBI:28044","CHEBI:16709","CHEBI:17822","CHEBI:16610","CHEBI:16765","CHEBI:17895","CHEBI:17172","CHEBI:16450","CHEBI:16027","CHEBI:17202","CHEBI:16695","CHEBI:17780","CHEBI:77138","CHEBI:16865","CHEBI:59640","CHEBI:142440","CHEBI:16708","CHEBI:16977","CHEBI:44549","CHEBI:29016","CHEBI:17196","CHEBI:16958","CHEBI:17285","CHEBI:15356","CHEBI:27470","CHEBI:15946","CHEBI:47987","CHEBI:4170","CHEBI:28300","CHEBI:16856","CHEBI:15428","CHEBI:15971","CHEBI:15699","CHEBI:18095","CHEBI:17596","CHEBI:1157","CHEBI:25017","CHEBI:16946","CHEBI:24898","CHEBI:18019","CHEBI:6650","CHEBI:15784","CHEBI:17981","CHEBI:15961","CHEBI:15811","CHEBI:14737","CHEBI:7916","CHEBI:26271","CHEBI:17148","CHEBI:16119","CHEBI:15978","CHEBI:68329","CHEBI:15891","CHEBI:36276","CHEBI:16857","CHEBI:16551","CHEBI:27897","CHEBI:16704","CHEBI:16414","CHEBI:18107"]}}