Summary of Study ST000929

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000643. The data can be accessed directly via it's Project DOI: 10.21228/M8JT38 This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000929
Study TitleMetabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices
Study TypeMetabolomics Evaluation of Aqueous Humor Samples from Left (treated) and Right (Control) Eyes of Rabbits.
Study SummaryMetabolomic 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
DepartmentNutrition Research Institute
LaboratoryERCMRC
Last NameSumner
First NameSusan
Address500 Laureate Way, Kannapolis, NC, 28081, USA
Emailsusan_sumner@unc.edu
Phone7042505066
Submit Date2018-02-11
Num Groups9
Total Subjects56
Num Males56
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8JT38
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000643
Project DOI:doi: 10.21228/M8JT38
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

Subject:

Subject ID:SU000968
Subject Type:Mammal
Subject Species:Oryctolagus cuniculus
Taxonomy ID:9986
Gender:Male

Factors:

Subject type: Mammal; Subject species: Oryctolagus cuniculus (Factor headings shown in green)

mb_sample_id local_sample_id Eye Treatment
SA055443Day153_IV-60L_POSLeft Eye 153 days post-valve implantation
SA055444Day153_IV-59L_POSLeft Eye 153 days post-valve implantation
SA055445Day153_IV-61L_POSLeft Eye 153 days post-valve implantation
SA055446Day153_IV-62L_POSLeft Eye 153 days post-valve implantation
SA055447Day153_IV-64L_POSLeft Eye 153 days post-valve implantation
SA055448Day153_IV-58L_POSLeft Eye 153 days post-valve implantation
SA055449Day153_IV-65L_POSLeft Eye 153 days post-valve implantation
SA055450Day27_L-X60-B_POSLeft Eye 27 days post-valve implantation
SA055451Day27_L-X59-B_POSLeft Eye 27 days post-valve implantation
SA055452Day27_L-X62-B_POSLeft Eye 27 days post-valve implantation
SA055453Day27_L-X64-B_POSLeft Eye 27 days post-valve implantation
SA055454Day27_L-X65-B_POSLeft Eye 27 days post-valve implantation
SA055455Day27_L-X58-B_POSLeft Eye 27 days post-valve implantation
SA055456Day27_L-X61-B_POSLeft Eye 27 days post-valve implantation
SA055457Day52_L-60-C_POSLeft Eye 52 days post-valve implantation
SA055458Day52_L-58-C_POSLeft Eye 52 days post-valve implantation
SA055459Day52_L-65-C_POSLeft Eye 52 days post-valve implantation
SA055460Day52_L-61-C_POSLeft Eye 52 days post-valve implantation
SA055461Day52_L-59-C_POSLeft Eye 52 days post-valve implantation
SA055462Day52_L-62-C_POSLeft Eye 52 days post-valve implantation
SA055463Day52_L-64-C_POSLeft Eye 52 days post-valve implantation
SA055464Day52_L-63-C_POSLeft Eye 52 days post-valve implantation
SA055465R_Pool_A2_POSPool from aqueous humor from control (right) eyes before surgery in the left eye. pre-valve implantation
SA055466R_Pool_A3_POSPool from aqueous humor from control (right) eyes before surgery in the left eye. pre-valve implantation
SA055467R_Pool_A1_POSPool from aqueous humor from control (right) eyes before surgery in the left eye. pre-valve implantation
SA055468L_Pool_A2_POSPool from aqueous humor from treated (left) eyes before valve implantation. pre-valve implantation
SA055469L_Pool_A1_POSPool from aqueous humor from treated (left) eyes before valve implantation. pre-valve implantation
SA055470L_Pool_A3_POSPool from aqueous humor from treated (left) eyes before valve implantation. pre-valve implantation
SA055471C_IV-58R_POSRight Eye control- 153 days post-valve
SA055472C_IV-65R_POSRight Eye control- 153 days post-valve
SA055473C_IV-60R_POSRight Eye control- 153 days post-valve
SA055474C_IV-64R_POSRight Eye control- 153 days post-valve
SA055475C_IV-59R_POSRight Eye control- 153 days post-valve
SA055476C_IV-62R_POSRight Eye control- 153 days post-valve
SA055477C_IV-61R_POSRight Eye control- 153 days post-valve
SA055478C_R-X59-B_POSRight Eye control- 27 days post-valve
SA055479C_R-X60-B_POSRight Eye control- 27 days post-valve
SA055480C_R-X61-B_POSRight Eye control- 27 days post-valve
SA055481C_R-X64-B_POSRight Eye control- 27 days post-valve
SA055482C_R-X58-B_POSRight Eye control- 27 days post-valve
SA055483C_R-X65-B_POSRight Eye control- 27 days post-valve
SA055484C_R-X62-B_POSRight Eye control- 27 days post-valve
SA055485C_R-60-C_POSRight Eye control- 52 days post-valve
SA055486C_R-63-C_POSRight Eye control- 52 days post-valve
SA055487C_R-61-C_POSRight Eye control- 52 days post-valve
SA055488C_R-64-C_POSRight Eye control- 52 days post-valve
SA055489C_R-65-C_POSRight Eye control- 52 days post-valve
SA055490C_R-62-C_POSRight Eye control- 52 days post-valve
SA055491C_R-59-C_POSRight Eye control- 52 days post-valve
SA055492C_R-58-C_POSRight Eye control- 52 days post-valve
SA055493Pool_1_POSTotal Pool Whole Study QC Pool _1
SA055494Pool_2_POSTotal Pool Whole Study QC Pool _2
SA055495Pool_3_POSTotal Pool Whole Study QC Pool _3
SA055496Pool_4_POSTotal Pool Whole Study QC Pool _4
SA055497Pool_5_POSTotal Pool Whole Study QC Pool _5
SA055498Pool_6_POSTotal Pool Whole Study QC Pool _6
Showing results 1 to 56 of 56

Collection:

Collection ID:CO000962
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 ID:TR000982
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.

Sample Preparation:

Sampleprep ID:SP000975
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

Combined analysis:

Analysis ID AN001523
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Synapt-G2-Si
Ion Mode POSITIVE
Units Compound Normalised Abundance

Chromatography:

Chromatography ID:CH001073
Chromatography Summary:Reversed-Phase Gradient Seperation
Instrument Name:Waters Acquity
Column Name:Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:8 °C
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
Internal Standard:L-Tryptophan-d5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
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
Chromatography Type:Reversed phase

MS:

MS ID:MS001403
Analysis ID:AN001523
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
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
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