{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001841","ANALYSIS_ID":"AN002984","VERSION":"1","CREATED_ON":"June 25, 2021, 8:13 am"},
"PROJECT":{"PROJECT_TITLE":"Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice","PROJECT_SUMMARY":"Naphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome Center","LABORATORY":"Fiehn Lab","LAST_NAME":"Stevens","FIRST_NAME":"Nathanial C.","ADDRESS":"451 Health Sciences Drive University of California Davis Davis, CA 95616","EMAIL":"ncstevens@ucdavis.edu","PHONE":"828-284-4315","FUNDING_SOURCE":"This study was funded by NIH Grant R01 ES020867, P30 ES023513, and U2C ES030158. During the preparation of this manuscript, Nathanial C. Stevens was supported by Grant Number T32 ES007059."},
"STUDY":{"STUDY_TITLE":"Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice (part II)","STUDY_SUMMARY":"Naphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome Center","LABORATORY":"Fiehn Lab","LAST_NAME":"Stevens","FIRST_NAME":"Nathanial C.","ADDRESS":"451 Health Sciences Drive University of California Davis Davis, CA 95616","EMAIL":"ncstevens@ucdavis.edu","PHONE":"828-284-4315"},
"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","GENDER":"Not applicable"},
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"Sample ID":"PA_F_CO_24h_096",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_08.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_24h_097",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_09.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_24h_098",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_099",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_100",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_101",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_102",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_MB_14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_103",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_2h_104",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_105",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_106",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_107",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_108",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_media_6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_109",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19H96.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_CO_6h_110",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19H97.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_111",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19H98.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_112",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19H99.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_113",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I01.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_114",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I02.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_115",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I03.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_24h_116",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I04.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_117",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I05.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_118",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I06.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_119",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I07.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_120",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I08.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_121",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I09.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_2h_122",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_123",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_124",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_125",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_126",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_127",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I15.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_F_NA_6h_128",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I16.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_129",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I21.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_130",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I22.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_131",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I23.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_132",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I24.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_133",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I25.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_24h_134",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I26.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_135",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I27.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_136",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I28.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_137",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I29.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_138",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I30.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_139",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I31.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_2h_140",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I32.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_141",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I33.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_142",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I34.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_143",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I35.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_144",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I36.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_145",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I37.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_CO_6h_146",
"Factors":{"treatment":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I38.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_147",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I39.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_148",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I40.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_149",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I41.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_150",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I42.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_151",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I43.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_24h_152",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I44.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_153",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I45.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_154",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I46.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_155",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I47.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_156",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I48.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_157",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I49.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_2h_158",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I50.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_159",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I51.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_160",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I52.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_161",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I53.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_162",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I54.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_163",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I55.raw"}
},
{
"Subject ID":"-",
"Sample ID":"PA_M_NA_6h_164",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I57.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_165",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I58.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_166",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I59.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_167",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I60.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_168",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I61.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_169",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I62.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_170",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I63.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_171",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I64.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_172",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I65.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_173",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I66.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_174",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I67.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_175",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_19I68.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_176",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_20001.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_177",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_20002.raw"}
},
{
"Subject ID":"-",
"Sample ID":"pool_178",
"Factors":{"treatment":"Naphthalene"},
"Additional sample data":{"RAW_FILE_NAME":"Lung_micro_HILIC_NEG_PA_20097.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"animals sacrificed 2, 6, and 24 hours following naphthalene treatment.","SAMPLE_TYPE":"Liver"},
"TREATMENT":{"TREATMENT_SUMMARY":"Subjects were divided by 2, 6, and 24 hours following naphthalene and control"},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200μl and 100-1000μl Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 MΩ pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500μl 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Biogenic amines by LC QTOF HILIC","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 6550","COLUMN_NAME":"Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"HILIC","MS_TYPE":"EI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"LC/MS parameters The LC/QTOFMS analyses are performed using an Agilent 1290 Infinity LC system (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat). Polar compounds are separated on an Acquity UPLC BEH Amide Column, 130Å, 1.7 µm, 2.1 mm X 150 mm maintained at 45°C at a flow-rate of 0.4 mL/min. Solvent pre-heating (Agilent G1316) was used. The mobile phases consist of: Water, 10 mM Ammonium Formate, 0.125% Formic Acid (A) and Acetonitrile: Water (95/5, v/v), 10 mM Ammonium Formate, 0.125% Formic Acid (B) The gradient is as follows: 0 min 100% (A); 0–2 min 100% (A); 2–7.7 min 30% (A); 7.7–9.5 min 60% (A); 9.5–10.3 min 70% (A); 10.3–12.8 min 0% (A); 12.8–16.8 min 0% (A. A sample volume of 1 µL for positive mode and 3 µL for negative mode is used for the injection. Sample temperature is maintained at 4°C in the autosampler. spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 50–1200. Number of cycles in MS1 is 1667 with cycle time of 500ms and accumulation time 475ms. Mass spectrometer parameters are as follows (positive mode) Gas Temp 300°C, gas pressures in psi units with : GS1 and GS2 50 psi, CUR: 35. ISVF is 4500V and DP and CE are 10V and 100 V."},
"MS_METABOLITE_DATA":{
"Units":"normalized peak height",
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}