{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000929","ANALYSIS_ID":"AN001523","VERSION":"1","CREATED_ON":"February 26, 2018, 3:58 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices","PROJECT_TYPE":"Metabolomics of the aqueous humor of rabbits with Ahmed Glaucoma Valve implantation.","PROJECT_SUMMARY":"Aqueous humor samples for metabolomics experiment were generated in the following manner: Eight adult male white rabbits were given seven days to acclimate to their environment. On day eight, an Ahmed Glaucoma Valve was implanted into the left eye of every rabbit. The un-operated right eye served as control. One rabbit was lost during the course of the study. After adequate anesthesia, aqueous humor samples were taken from both eyes of each rabbit before surgery (A samples), and at 27 (B samples), 52 (C samples) and 153 days (IV samples) after surgery.","INSTITUTE":"Tulane University School of Medicine","DEPARTMENT":"Ophthalmology","LAST_NAME":"Ayyala","FIRST_NAME":"Ramesh S.","ADDRESS":"1430 Tulane Ave., New Orleans, LA 70112","EMAIL":"rayyala@tulane.edu","PHONE":"504-998-2261"},

"STUDY":{"STUDY_TITLE":"Metabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices","STUDY_TYPE":"Metabolomics Evaluation of Aqueous Humor Samples from Left (treated) and Right (Control) Eyes of Rabbits.","STUDY_SUMMARY":"Metabolomic experiments were carried out on aqueous humor samples provided by Ramesh Ayyala. Through this collaboration, we propose to study aqueous humor from control and experimental rabbits to better understand metabolic differences in the aqueous humor samples.","INSTITUTE":"University of North Carolina at Chapel Hill","DEPARTMENT":"Nutrition Research Institute","LABORATORY":"ERCMRC","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"500 Laureate Way, Kannapolis, NC, 28081, USA","EMAIL":"susan_sumner@unc.edu","PHONE":"7042505066","NUM_GROUPS":"9","TOTAL_SUBJECTS":"56","NUM_MALES":"56"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Oryctolagus cuniculus","TAXONOMY_ID":"9986","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"C_IV-58R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-59R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-60R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-61R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-62R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-64R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_IV-65R_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 153 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-58-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-59-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-60-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-61-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-62-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-63-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-64-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-65-C_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 52 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X58-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X59-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X60-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X61-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X62-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X64-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"C_R-X65-B_POS",
"Factors":{"Eye":"Right Eye","Treatment":"control- 27 days post-valve"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-58L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-59L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-60L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-61L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-62L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-64L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day153_IV-65L_POS",
"Factors":{"Eye":"Left Eye","Treatment":"153 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X58-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X59-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X60-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X61-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X62-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X64-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day27_L-X65-B_POS",
"Factors":{"Eye":"Left Eye","Treatment":"27 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-58-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-59-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-60-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-61-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-62-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-63-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-64-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Day52_L-65-C_POS",
"Factors":{"Eye":"Left Eye","Treatment":"52 days post-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"L_Pool_A1_POS",
"Factors":{"Eye":"Pool from aqueous humor from treated (left) eyes before valve implantation.","Treatment":"pre-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"L_Pool_A2_POS",
"Factors":{"Eye":"Pool from aqueous humor from treated (left) eyes before valve implantation.","Treatment":"pre-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"L_Pool_A3_POS",
"Factors":{"Eye":"Pool from aqueous humor from treated (left) eyes before valve implantation.","Treatment":"pre-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_1_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _1"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_2_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _2"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_3_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _3"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_4_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _4"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_5_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _5"}
},
{
"Subject ID":"-",
"Sample ID":"Pool_6_POS",
"Factors":{"Eye":"Total Pool","Treatment":"Whole Study QC Pool _6"}
},
{
"Subject ID":"-",
"Sample ID":"R_Pool_A1_POS",
"Factors":{"Eye":"Pool from aqueous humor from control (right) eyes before surgery in the left eye.","Treatment":"pre-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"R_Pool_A2_POS",
"Factors":{"Eye":"Pool from aqueous humor from control (right) eyes before surgery in the left eye.","Treatment":"pre-valve implantation"}
},
{
"Subject ID":"-",
"Sample ID":"R_Pool_A3_POS",
"Factors":{"Eye":"Pool from aqueous humor from control (right) eyes before surgery in the left eye.","Treatment":"pre-valve implantation"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Aqueous humor was collected from both eyes before surgery, then at one month, two months, and five months post operatively. After adequate anesthesia the eye was prepped with 5% betadine solution and then covered with a sterile drape. A sterile 27G needle was inserted into the anterior chamber through the clear cornea of the para-limbal area. Approximately 0.1 ml of aqueous humor was acquired in each collection cycle. The samples were immediately placed over an ice bath then transferred to a freezer for storage at -70ºC.","SAMPLE_TYPE":"aqueous humour"},

"TREATMENT":{"TREATMENT_SUMMARY":"A Glaucoma Drainage Device was inserted into the left eye of each of Eight Rabbits. Aqueous humor was collected from the left (treated) eye and right (control) eye before implantation and at several time points after surgey."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Whole Study Pooled QC Thawed aqueous humor samples on ice. Whole study pooled QC samples were created by combining 10 µL aliquot from each of the study samples (Time Points B, C and D) into a 2 mL Lo-Bind eppendorf tube. The QC pooled sample was then vortexed for 30 seconds. Time Point A Pools Aqueous humor samples were collected from both, right and left, eyes and provided for metabolomics analysis. Aqueous humor from the right eyes from experiment A were combined into a 2 mL Lo-Bind Eppendorf tube to make a right eye pool from experiment A. This same procedure was repeated to make a pool from the left eye aqueous humor from experiment A. The two time point A pools were vortexed for 30 seconds. Sample Preparation To make the study samples, aqueous humor (30 µL) was transferred from their original tubes into 2.0 mL Lo-Bind Eppendorf tubes. Six whole study pooled QC samples of 30 µL each were created along with three-30 µL time point A pool from right eye and three-30 µL time point A pool from left eye aqueous humor. For all samples (study, whole study pooled QC and time point A samples) 400 µL Protein Precipitation Buffer with internal standard (0.025 mg/mL of Tryptophan-d5 in methanol) was added to each tube and vortexed. The samples were then centrifuged at 16,000 rcf for 4 min. A 350 µL aliquot of the supernatant from each sample was transferred into pre-labeled 2.0 mL LoBind eppendorf tube and stored at -80 °C for one hour followed by a drying step on a lyophilizer. The residue was reconstituted in 100 µL of reconstitution buffer (95:5 Water:Methanol, v/v) and mixed on a multiple tube vortexer for 10 min at 5,000 rpm. Then, the samples were centrifuged at room temperature for 4 min at 16,000 rcf, and the supernatants were transferred to autosampler vials for data acquisition.","SAMPLEPREP_PROTOCOL_ID":"Protocol: RTI-RCMRC-LCMS-SA-018 Version: 1.0","SAMPLEPREP_PROTOCOL_FILENAME":"18 AP-Williamson-Aqueous humor-RTI-RCMRC-LCMS-SA-018_v1.0.docx","PROCESSING_METHOD":"Protein Precipitation followed by Metabolite Extraction and Lyophilization","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"Cold Methanol with Internal Standard","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"95:5 Water:Methanol","SAMPLE_SPIKING":"L-Tryptophan-d5"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Reversed-Phase Gradient Seperation","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)","FLOW_GRADIENT":"Time(min) Flow Rate(mL/min) %A %B Curve 1. Initial 0.400 99.0 1.0 2. 1.00 0.400 99.0 1.0 3. 16.00 0.400 1.0 99.0 4. 20.00 0.400 1.0 99.0 5. 20.50 0.400 99.0 1.0 6. 22.00 0.400 99.0 1.0","FLOW_RATE":"0.4 mL/min","COLUMN_TEMPERATURE":"8 °C","SOLVENT_A":"Water with 0.1% formic acid","SOLVENT_B":"Methanol with 0.1% formic acid","INTERNAL_STANDARD":"L-Tryptophan-d5","ANALYTICAL_TIME":"22 min","WEAK_WASH_SOLVENT_NAME":"10% MeOH","WEAK_WASH_VOLUME":"1000 µL","STRONG_WASH_SOLVENT_NAME":"80% MeOH","STRONG_WASH_VOLUME":"1000 µL","TARGET_SAMPLE_TEMPERATURE":"8 °C","SAMPLE_LOOP_SIZE":"10 µL","SAMPLE_SYRINGE_SIZE":"100 µL","RANDOMIZATION_ORDER":"Yes"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"ERCMRC","OPERATOR_NAME":"James Carlson","DETECTOR_TYPE":"TOF","SOFTWARE_VERSION":"MassLynx 4.1","ACQUISITION_DATE":"2/13/2015-2/14/2015"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Waters Synapt G2 Si QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","ACQUISITION_DATE":"2/13/2015-2/14/2015","CAPILLARY_TEMPERATURE":"110 °C","CAPILLARY_VOLTAGE":"1.0 kV","COLLISION_ENERGY":"4","FRAGMENTATION_METHOD":"CID","HELIUM_FLOW":"180","IONIZATION":"ES+","MASS_ACCURACY":"5 ppm","SOURCE_TEMPERATURE":"100 °C","DATAFORMAT":"Continuum","DESOLVATION_GAS_FLOW":"400 L/Hr","DESOLVATION_TEMPERATURE":"400 °C","RESOLUTION_SETTING":"18000","SCAN_RANGE_MOVERZ":"50-1000 m/z","SCANNING_CYCLE":"1.0 s","TUBE_LENS_VOLTAGE":"75","MS_RESULTS_FILE":"ST000929_AN001523_Results.txt UNITS:Compound Normalised Abundance"}

}