{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000627","ANALYSIS_ID":"AN000959","VERSION":"1","CREATED_ON":"08-28-2017"}, "PROJECT":{"PROJECT_TITLE":"A strategy for producing a searchable bronchoalveolar lavage fluid compound database","PROJECT_TYPE":"MS","PROJECT_SUMMARY":"Comprehensive metabolomic databases for Lipid(+/-) and Aqueous(+) fractions of BALF assembled from a mouse and human COPD experiment.","INSTITUTE":"University of Colorado, Denver","DEPARTMENT":"Pharmaceutical Sciences, Anschutz Medical Campus","LABORATORY":"Metabolomics and Mass Spectrometry","LAST_NAME":"Residorph","FIRST_NAME":"Nichole","ADDRESS":"12850 East Montview Blvd, Denver, CO 80204","EMAIL":"nichole.reisdorph@ucdenver.edu","PHONE":"-","FUNDING_SOURCE":"P20-HL113445 Metabolic Profiles of COPD phenotypes"}, "STUDY":{"STUDY_TITLE":"Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Lipid(+) experiment (part III)","STUDY_TYPE":"Comprehensive profile","STUDY_SUMMARY":"Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64)","INSTITUTE":"University of Colorado Anschutz Medical Campus","DEPARTMENT":"Pharmaceutical Sciences","LABORATORY":"Metabolomics and Mass Spectrometry","LAST_NAME":"Residorph","FIRST_NAME":"Nichole","ADDRESS":"12850 East Montview Blvd, Denver, CO 80204","EMAIL":"nichole.reisdorph@ucdenver.edu","PHONE":"-","NUM_GROUPS":"2","TOTAL_SUBJECTS":"42"}, "SUBJECT":{"SUBJECT_TYPE":"Human;Animal","SUBJECT_SPECIES":"Homo sapiens;Mus musculus","TAXONOMY_ID":"9606 | 10093","GENOTYPE_STRAIN":"Animal: C57BL/6"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"11833", "Sample ID":"BALF_11833_15uL_A", "Factors":{"Species":"Human","SmokingStatus":"Former smoker","Phenotype":"Moderate"}, "Additional sample data":{"Gender":"M","Replicate":"A","Spike":"-"} }, { "Subject ID":"11833", "Sample ID":"BALF_11833_15uL_B", "Factors":{"Species":"Human","SmokingStatus":"Former smoker","Phenotype":"Moderate"}, "Additional sample data":{"Gender":"M","Replicate":"B","Spike":"-"} }, { "Subject ID":"11833", "Sample ID":"BALF_11833_15uL_C", "Factors":{"Species":"Human","SmokingStatus":"Former smoker","Phenotype":"Moderate"}, "Additional sample data":{"Gender":"M","Replicate":"C","Spike":"-"} }, { "Subject ID":"10031", "Sample ID":"BALF_10031_15uL_A", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"-"} }, { "Subject ID":"10031", "Sample ID":"BALF_10031_15uL_B", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"-"} }, { "Subject ID":"10031", "Sample ID":"BALF_10031_15uL_C", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"-"} }, { "Subject ID":"17800", "Sample ID":"BALF_17800_15uL_A", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"M","Replicate":"A","Spike":"-"} }, { "Subject ID":"17800", "Sample ID":"BALF_17800_15uL_B", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"M","Replicate":"B","Spike":"-"} }, { "Subject ID":"17800", "Sample ID":"BALF_17800_15uL_C", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"COPD"}, "Additional sample data":{"Gender":"M","Replicate":"C","Spike":"-"} }, { "Subject ID":"12558", "Sample ID":"BALF_12558_15uL_A", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"A","Spike":"-"} }, { "Subject ID":"12558", "Sample ID":"BALF_12558_15uL_B", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"B","Spike":"-"} }, { "Subject ID":"12558", "Sample ID":"BALF_12558_15uL_C", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"C","Spike":"-"} }, { "Subject ID":"14442", "Sample ID":"BALF_14442_15uL_A", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"A","Spike":"-"} }, { "Subject ID":"14442", "Sample ID":"BALF_14442_15uL_B", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"B","Spike":"-"} }, { "Subject ID":"14442", "Sample ID":"BALF_14442_15uL_C", "Factors":{"Species":"Human","SmokingStatus":"Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"M","Replicate":"C","Spike":"-"} }, { "Subject ID":"MET133", "Sample ID":"BALF_MET133_1x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"1x"} }, { "Subject ID":"MET133", "Sample ID":"BALF_MET133_1x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"1x"} }, { "Subject ID":"MET133", "Sample ID":"BALF_MET133_1x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"1x"} }, { "Subject ID":"MET141", "Sample ID":"BALF_MET141_2x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"2x"} }, { "Subject ID":"MET141", "Sample ID":"BALF_MET141_2x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"2x"} }, { "Subject ID":"MET141", "Sample ID":"BALF_MET141_2x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"2x"} }, { "Subject ID":"MET142", "Sample ID":"BALF_MET142_4x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"4x"} }, { "Subject ID":"MET142", "Sample ID":"BALF_MET142_4x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"4x"} }, { "Subject ID":"MET142", "Sample ID":"BALF_MET142_4x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"4x"} }, { "Subject ID":"MET143", "Sample ID":"BALF_MET143_1x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"1x"} }, { "Subject ID":"MET144", "Sample ID":"BALF_MET144_2x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"2x"} }, { "Subject ID":"MET144", "Sample ID":"BALF_MET144_2x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"2x"} }, { "Subject ID":"MET144", "Sample ID":"BALF_MET144_2x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Non-Smoker","Phenotype":"Healthy"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"2x"} }, { "Subject ID":"MET106", "Sample ID":"BALF_MET106_4x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"4x"} }, { "Subject ID":"MET106", "Sample ID":"BALF_MET106_4x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"4x"} }, { "Subject ID":"MET106", "Sample ID":"BALF_MET106_4x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"4x"} }, { "Subject ID":"MET107", "Sample ID":"BALF_MET107_1x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"1x"} }, { "Subject ID":"MET107", "Sample ID":"BALF_MET107_1x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"1x"} }, { "Subject ID":"MET108", "Sample ID":"BALF_MET108_2x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"2x"} }, { "Subject ID":"MET108", "Sample ID":"BALF_MET108_2x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"2x"} }, { "Subject ID":"MET108", "Sample ID":"BALF_MET108_2x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"2x"} }, { "Subject ID":"MET126", "Sample ID":"BALF_MET126_4x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"4x"} }, { "Subject ID":"MET126", "Sample ID":"BALF_MET126_4x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"4x"} }, { "Subject ID":"MET126", "Sample ID":"BALF_MET126_4x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"4x"} }, { "Subject ID":"MET128", "Sample ID":"BALF_MET128_1x_lipid_pos_A", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"A","Spike":"1x"} }, { "Subject ID":"MET128", "Sample ID":"BALF_MET128_1x_lipid_pos_B", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"B","Spike":"1x"} }, { "Subject ID":"MET128", "Sample ID":"BALF_MET128_1x_lipid_pos_C", "Factors":{"Species":"Mouse","SmokingStatus":"Smoker","Phenotype":"Emphysema"}, "Additional sample data":{"Gender":"F","Replicate":"C","Spike":"1x"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Mouse BALF collection was performed using a total of 1.0 mL PBS divided into three washes and stored at -80°C until analysis. Human BALF was collected in the right middle lobe and lingual by instilling two aliquots of 40 mL and one aliquot of 50 mL of sterile saline per lobe (i.e., 130 mL per lobe, total volume?=?260 mL per subject), which is withdrawn by gentle manual suction and immediately placed on ice. Aliquots for metabolomics analysis were frozen at -80 °C and stored until sample preparation and MS analysis.","SAMPLE_TYPE":"BALF","COLLECTION_METHOD":"Broncheoalveolar lavage"}, "TREATMENT":{"TREATMENT_SUMMARY":"None"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"100uL of BALF were prepared using methanol assisted protein precipitation followed by methyl-tert butyl ether (MTBE) liquid-liquid extraction. Both liquid and aqueous fractions were preserved for analysis. The lipid fraction was reconstituted in 200µL of methanol. The lipid fraction was dried down in a SpeedVac at 45°C for reconstitution in 50 µL of 95:5 water:acetonitrile."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The BALF samples were separated using C18 reverse phase chromatography. The separations used an Agilent Zorbax Rapid Resolution HD (RRHD) SB-C18, 1.8 micron (2.1 x 100 mm) analytical column with an Agilent Zorbax SB-C18, 1.8 micron (2.1 x 5 mm) guard column and used an Agilent 1290 series high performance liquid chromatography (HPLC) pump. Injection volumes were 4µL for mouse BALF and 15µL for human BALF. Flow rate was 0.7 mL/min using the following mobile phases: mobile phase A was water with 0.1% formic acid, and mobile phase B was 60:36:4 isopropyl alcohol:acetonitrile:water with 0.1% formic acid. Gradients were 0-0.5 minutes 30-70% B, 0.5-7.42 minutes 70-100% B, 7.42-9.9 minutes 100% B, 9.9-10.0 minutes 100-30% B, 10-14.6 minutes 30% B for the positive mode injections. For negative mode the following eluant profile was used: 0-1 minutes 30-70% B, 1-7.92 minutes 70-100% B, 7.92-10.4 minutes 100% B, 10.4-10.5 minutes 100-30% B, 10.5-15.1 minutes 30% B.","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"Agilent Zorbax RRHD SB-C18 (100 x 2.1mm, 1.8um) analytical column with an Agilent Zorbax SB-C18, 1.8 micron (2.1 x 5 mm) guard column","FLOW_RATE":"0.7ml/min","CHROMATOGRAPHY_TYPE":"Reversed phase"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6510 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_VOLTAGE":"4000V","FRAGMENT_VOLTAGE":"120","DESOLVATION_GAS_FLOW":"12mL/min","DESOLVATION_TEMPERATURE":"300C","NEBULIZER":"30psi","SCAN_RANGE_MOVERZ":"60-1600","SCANNING":"2.02 spectra/second","SKIMMER_VOLTAGE":"60V"} }