{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003759","ANALYSIS_ID":"AN006173","PROJECT_ID":"PR002342","VERSION":"1","CREATED_ON":"February 28, 2025, 12:51 pm"},

"PROJECT":{"PROJECT_TITLE":"Analysis of metabolite levels in the circulation of pancreatic tumor bearing mice with or without depletion of myeloid cells","PROJECT_SUMMARY":"In this study, we assessed the impact of myeloid cells on the levels of circulating metabolites in the plasma of mice bearing tumors. To do so, murine pancreatic ductal adenocarcinoma (PDAC) cells were implanted into C57Bl6J CD11b-DTR host animals. Myeloid cells were then ablated with 25 ng/g diptheria toxin (DT). Serum from DT treated mice was collected for analysis. Additionally, serum was collected from PDAC bearing mice that were vehicle treated. This data allows for identification of how myeloid cells in tumor bearing mice contribute to levels of circulating metabolites.","INSTITUTE":"University of Chicago","DEPARTMENT":"Ben May Department for Cancer Research","LAST_NAME":"Muir","FIRST_NAME":"Alexander","ADDRESS":"929 E 57th St","EMAIL":"amuir@uchicago.edu","PHONE":"7738346506"},

"STUDY":{"STUDY_TITLE":"Analysis of metabolite levels in the circulation of pancreatic tumor bearing mice with or without depletion of myeloid cells","STUDY_SUMMARY":"In this study, we assessed the impact of myeloid cells on the levels of circulating metabolites in the plasma of mice bearing tumors. To do so, murine pancreatic ductal adenocarcinoma (PDAC) cells were implanted into C57Bl6J CD11b-DTR host animals. Myeloid cells were then ablated with 25 ng/kg diptheria toxin (DT). Serum from DT treated mice was collected for analysis. Additionally, serum was collected from PDAC bearing mice that were vehicle treated. This data allows for identification of how myeloid cells in tumor bearing mice contribute to levels of circulating metabolites.","INSTITUTE":"University of Chicago","LAST_NAME":"Muir","FIRST_NAME":"Alexander","ADDRESS":"929 E 57th St","EMAIL":"amuir@uchicago.edu","PHONE":"7738346506"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"serum_DT_1",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_35.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_DT_2",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_36.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_DT_3",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_37.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_DT_4",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_38.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_DT_5",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_39.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_DT_6",
"Factors":{"Sample source":"Blood serum","Treatment":"Diptheria_toxin"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_40.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_1",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_47.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_2",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_48.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_3",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_49.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_4",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_50.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_5",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_51.raw"}
},
{
"Subject ID":"-",
"Sample ID":"serum_noDT_6",
"Factors":{"Sample source":"Blood serum","Treatment":"vehicle"},
"Additional sample data":{"RAW_FILE_NAME(Raw_data_file_name)":"190723_QE2_AlexanderMuir_Job1623_52.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were euthanised 24 hours after treatment by CO2 asphyxiation and blood collected through cardiac puncture. Serum was isolated using BD microtainer serum separator tubes as per manufactures’ instructions and stored at -80 until analysis.","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"CD11b-DTR mice were produced as an F1 cross between B6.FVB-Tg(ITGAM-DTR/EGFP)34Lan/J mice and C57BL/6J mice (Jackson Laboratory). Male mice between 8-12 weeks of age were used experimentally. Orthotopic PDAC tumours were established from 5x104 KPC-7940B PDAC cells injected into the pancreas were established as tumors for 14 days. Mice were then treated with diphtheria toxin (Enzo Life Science) at a concentration of 25 ng/kg or vehicle by intraperitoneal injection. Mice were euthanised 24 hours after treatment by CO2 asphyxiation and blood collected through cardiac puncture. Serum was isolated using BD microtainer serum separator tubes as per manufactures’ instructions and stored at -80 until analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites were quantified as described in Sullivan et al eLife 2019 (PMID: 30990168). Briefly, in order to quantitate metabolites in serum samples, we first constructed a library of 149 chemical standards of plasma polar metabolites. These compounds were selected to encompass a number of metabolic processes and have previously been included in efforts to profile plasma polar metabolites by LC/MS (Cantor et al., 2017; Evans et al., 2009; Lawton et al., 2008; Mazzone et al., 2016). We pooled these metabolites into 7 separate chemical standard pools. To do this, each metabolite in a given pool was weighed and then mixed (6 cycles of 1 min. mixing at 25 Hz followed by 3 min. resting) using a Mixer Mill MM301 (Retsch, Düsseldorf, Germany), and mixed metabolite powder stocks were stored at -20°C prior to resuspension and analysis. Stock solutions of the mixed standards pools containing ~5mM, ~1mM, ~300µM, ~100µM, ~30µM, ~10µM, ~3µM and ~1µM of each metabolite were made in HPLC grade water and were stored at -80°C. We refer to these stock solutions as “external standard pools” throughout. External standard pools were used to confirm the retention time and m/z for each analyte and provide standards to quantitate concentrations of stable isotope labeled internal standards used in downstream analysis, as well as to quantitate metabolite concentrations in TIF and plasma samples directly where internal standards were not available (see below for details). To extract polar metabolites from plasma, TIF or the external standard pools, 5µL of serum or external sample pools was mixed with 45uL of acetonitrile:methanol:formic acid (75:25:0.1) extraction buffer including the following isotopically labeled internal standards: 13C labeled yeast extract (Cambridge Isotope Laboratory, Andover, MA, ISO1), 13C3 lactate (Sigma Aldrich, Darmstadt, Germany, 485926), 13C3 glycerol (Cambridge Isotope Laboratory, Andover, MA, CLM-1510), 13C6 15N2 cystine (Cambridge Isotope Laboratory, Andover, MA, CNLM-4244), 2H9 choline (Cambridge Isotope Laboratory, Andover, MA, DLM-549), 13C4 3-hydroxybutyrate (Cambridge Isotope Laboratory, Andover, MA, CLM-3853), 13C6 glucose (Cambridge Isotope Laboratory, Andover, MA, CLM-1396), 13C2 15N taurine (Cambridge Isotope Laboratory, Andover, MA, CNLM-10253), 2H3 creatinine (Cambridge Isotope Laboratory, Andover, MA, DLM-3653), 8-13C adenine (Cambridge Isotope Laboratory, Andover, MA, CLM-1654), 13C5 hypoxanthine (Cambridge Isotope Laboratory, Andover, MA, CLM-8042), 8-13C guanine (Cambridge Isotope Laboratory, Andover, MA, CLM-1019), 13C3 serine (Cambridge Isotope Laboratory, Andover, MA, CLM-1574) and 13C2 glycine (Cambridge Isotope Laboratory, Andover, MA, CLM-1017). All solvents used in the extraction buffer were HPLC grade. Samples were then vortexed for 10 min. at 4°C and insoluble material was sedimented by centrifugation at 15kg for 10 min. at 4°C. 20µL of the soluble polar metabolite extract was taken for LC/MS analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"SeQuant ZIC-pHILIC (150 x 2.1mm,5um)","SOLVENT_A":"100% water; 20 mM ammonium carbonate, 0.1% ammonium hydroxide","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"linear gradient from 80% to 20% B; 20-20.5 min: linear gradient from 20% to 80% B; 20.5-28min: hold at 80% B.","FLOW_RATE":"0.150 mL/min","COLUMN_TEMPERATURE":"25"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"LC/MS analysis was performed using a QExactive orbitrap mass spectrometer using an Ion Max source and heated electrospray ionization (HESI) probe coupled to a Dionex Ultimate 3000 UPLC system (Thermo Fisher Scientific, Waltham, MA). External mass calibration was performed every 7 days. 2μL of each sample was injected onto a ZIC-pHILIC 2.1 × 150 mm analytical column equipped with a 2.1 × 20 mm guard column (both 5 μm particle size, EMD Millipore). The autosampler and column oven were held at 4°C and 25°C, respectively. Buffer A was 20 mM ammonium carbonate, 0.1% ammonium hydroxide; buffer B was acetonitrile. The chromatographic gradient was run at a flow rate of 0.150 mL/min as follows: 0-20 min: linear gradient from 80% to 20% B; 20-20.5 min: linear gradient from 20% to 80% B; 20.5-28min: hold at 80% B. The mass spectrometer was operated in full scan, polarity-switching mode with the spray voltage set to 3.0 kV, the heated capillary held at 275°C, and the HESI probe held at 350°C. The sheath gas flow rate was set to 40 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 1 unit. The MS data acquisition was performed in a range of 70-1000 m/z, with the resolution set to 70,000, the AGC target at 1e6, and the maximum injection time at 20 msec. Metabolite identification and quantification was performed with XCalibur 2.2 software (Thermo Fisher Scientific, Waltham, MA) using a 5ppm mass accuracy and a 0.5 min. retention time window. For metabolite identification, external standard pools were used for assignment of metabolites to peaks at given m/z and retention time, and to determine the limit of detection for each metabolite. Metabolite quantification was performed by two separate methods. Where internal standards were available, first, comparison of the peak areas of the stable isotope labeled internal standards with the external standard pools allowed for quantification of the concentration of labeled internal standards in the extraction buffer. Subsequently, we compared the peak area of a given metabolite in the TIF and plasma samples with the peak area of the internal standard to quantitate the concentration of that metabolite in the serum sample. For metabolites without internal standards, the peak area of each analyte was normalized to the peak area of a labeled amino acid internal standard that eluted at roughly the same retention time to account for differences in recovery between samples. From the normalized peak areas of metabolites in the external standard pools, we generated a standard curve describing the relationship between metabolite concentration and normalized peak area. The standard curves were linear with fits typically at or above r2=0.95. Metabolites which did not meet these criteria were excluded from further analysis. These equations were then used to convert normalized peak areas of analytes in the serum samples into analyte concentration in the samples. The relationship between metabolite concentration and normalized peak area is matrix dependent, and the external standards are prepared in water, which is a different matrix than serum. Therefore, we consider metabolite measurements using this external standard method semi-quantitative."},

"MS_METABOLITE_DATA":{
"Units":"micromole/L",

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"Metabolites":[{"metabolite_name":"3-methyl-2-oxopentanoic-acid-ketoisoleucine"},{"metabolite_name":"3-methyl-2-oxobutyrate-keto-isovaleric-acid"},{"metabolite_name":"pipecolate"},{"metabolite_name":"orotate"},{"metabolite_name":"2HG"},{"metabolite_name":"UDP-GlcNAc"},{"metabolite_name":"pyruvate"},{"metabolite_name":"succinate"},{"metabolite_name":"akg"},{"metabolite_name":"malate"},{"metabolite_name":"glucose-6-phosphate"},{"metabolite_name":"citrate"},{"metabolite_name":"uridine"},{"metabolite_name":"AMP"},{"metabolite_name":"a-aminobutyrate"},{"metabolite_name":"argininosuccinate"},{"metabolite_name":"GMP"},{"metabolite_name":"lactate"},{"metabolite_name":"glucose"},{"metabolite_name":"serine"},{"metabolite_name":"glutamate"},{"metabolite_name":"aspartate"},{"metabolite_name":"taurine"},{"metabolite_name":"aKB"},{"metabolite_name":"formyl-methionine"},{"metabolite_name":"aHB"},{"metabolite_name":"mannose"},{"metabolite_name":"3-hydroxyisobutyric acid"},{"metabolite_name":"FAD"},{"metabolite_name":"uric acid"},{"metabolite_name":"cysteic acid"},{"metabolite_name":"carbamoylaspartate"},{"metabolite_name":"uracil"},{"metabolite_name":"fumarate"},{"metabolite_name":"DHAP"},{"metabolite_name":"3-phosphoglycerate"},{"metabolite_name":"cis-aconitate"},{"metabolite_name":"thymidine"},{"metabolite_name":"acetylglycine"},{"metabolite_name":"ribose-5-phosphate"},{"metabolite_name":"ATP"},{"metabolite_name":"dCTP"},{"metabolite_name":"UTP"},{"metabolite_name":"CTP"},{"metabolite_name":"GTP"},{"metabolite_name":"p-aminobenzoate"},{"metabolite_name":"glycerate"},{"metabolite_name":"sorbitol"},{"metabolite_name":"allantoin"},{"metabolite_name":"myo-inositol"},{"metabolite_name":"UDP-glucose"},{"metabolite_name":"2-hydroxybutyrate"},{"metabolite_name":"thiamine"},{"metabolite_name":"xanthine"},{"metabolite_name":"fructose"},{"metabolite_name":"dTMP"},{"metabolite_name":"o-phosphoethanolamine"},{"metabolite_name":"glucose-1-phosphate"}]
}

}