Summary of Study ST001278

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 PR000863. The data can be accessed directly via it's Project DOI: 10.21228/M84M57 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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.

Show all samples
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)

Study ID	ST001278
Study Title	POAG and Control Aqueous Humor IROA Metabolites from Veterans Affairs Patients
Study Type	untargeted LC-MS/MS metabolomics IROA
Study Summary	We performed high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of the metabolome of POAG and Control patients. Samples were collected asynchronously.
Institute	University of Miami
Department	Ophthalmology, Bascom Palmer Eye Institute
Laboratory	Sanjoy K. Bhattacharya
Last Name	Bhattacharya
First Name	Sanjoy
Address	1638 NW 10th Avenue, Miami, FL 33136
Email	SBhattacharya@med.miami.edu
Phone	305-482-4103
Submit Date	2019-11-14
Num Groups	2
Total Subjects	41
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2020-05-14
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000863
Project DOI:	doi: 10.21228/M84M57
Project Title:	POAG and Control Aqueous Humor IROA Metabolites from Veterans Affairs Patients
Project Type:	untargeted LC-MS/MS IROA metabolomics
Project Summary:	We performed high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Isotopic Ratio Outlier Analysis (IROA) data analysis on aqueous humor patient samples. Samples were collected at asynchronous times.
Institute:	University of Miami
Department:	Ophthalmology, Bascom Palmer Eye Institute
Laboratory:	Sanjoy K. Bhattacharya
Last Name:	Bhattacharya
First Name:	Sanjoy
Address:	1638 NW 10th Avenue, Miami, Florida, 33136, USA
Email:	sbhattacharya@med.miami.edu
Phone:	3054824103
Contributors:	Leila Abdelrahman

Subject:

Subject ID:	SU001350
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Factor
SA093297	S0016_POS	Control
SA093298	S0015_POS	Control
SA093299	S0013_POS	Control
SA093300	S0017_POS	Control
SA093301	S0014_POS	Control
SA093302	S0018_POS	Control
SA093303	S0021_POS	Control
SA093304	S0020_POS	Control
SA093305	S0019_POS	Control
SA093306	S0012_POS	Control
SA093307	S0011_POS	Control
SA093308	S0005_POS	Control
SA093309	S0004_POS	Control
SA093310	S0003_POS	Control
SA093311	S0006_POS	Control
SA093312	S0007_POS	Control
SA093313	S0010_POS	Control
SA093314	S0009_POS	Control
SA093315	S0008_POS	Control
SA093316	S0022_POS	Control
SA093317	S0023_POS	Control
SA093318	S0036_POS	Control
SA093319	S0035_POS	Control
SA093320	S0034_POS	Control
SA093321	S0037_POS	Control
SA093322	S0038_POS	Control
SA093323	S0041_POS	Control
SA093324	S0040_POS	Control
SA093325	S0039_POS	Control
SA093326	S0033_POS	Control
SA093327	S0032_POS	Control
SA093328	S0026_POS	Control
SA093329	S0025_POS	Control
SA093330	S0024_POS	Control
SA093331	S0027_POS	Control
SA093332	S0028_POS	Control
SA093333	S0031_POS	Control
SA093334	S0030_POS	Control
SA093335	S0029_POS	Control
SA093336	S0002_POS	Control
SA093337	S0001_POS	Control
SA093338	S0025_NEG	Control
SA093339	S0024_NEG	Control
SA093340	S0026_NEG	Control
SA093341	S0027_NEG	Control
SA093342	S0028_NEG	Control
SA093343	S0023_NEG	Control
SA093344	S0021_NEG	Control
SA093345	S0017_NEG	Control
SA093346	S0018_NEG	Control
SA093347	S0019_NEG	Control
SA093348	S0020_NEG	Control
SA093349	S0029_NEG	Control
SA093350	S0022_NEG	Control
SA093351	S0039_NEG	Control
SA093352	S0037_NEG	Control
SA093353	S0040_NEG	Control
SA093354	S0041_NEG	Control
SA093355	S0030_NEG	Control
SA093356	S0036_NEG	Control
SA093357	S0038_NEG	Control
SA093358	S0033_NEG	Control
SA093359	S0032_NEG	Control
SA093360	S0034_NEG	Control
SA093361	S0031_NEG	Control
SA093362	S0035_NEG	Control
SA093363	S0006_NEG	POAG
SA093364	S0007_NEG	POAG
SA093365	S0008_NEG	POAG
SA093366	S0005_NEG	POAG
SA093367	S0004_NEG	POAG
SA093368	S0002_NEG	POAG
SA093369	S0003_NEG	POAG
SA093370	S0009_NEG	POAG
SA093371	S0016_NEG	POAG
SA093372	S0015_NEG	POAG
SA093373	S0001_NEG	POAG
SA093374	S0014_NEG	POAG
SA093375	S0013_NEG	POAG
SA093376	S0011_NEG	POAG
SA093377	S0012_NEG	POAG
SA093378	S0010_NEG	POAG

Showing results 1 to 82 of 82

Showing results 1 to 82 of 82

Collection:

Collection ID:	CO001344
Collection Summary:	Aqueous Humor samples of VA patients with POAG and Control were taken.
Sample Type:	Eye tissue
Collection Method:	All materials were collected from human donors without identifiers under institutional review board exemption/approval. We acquired 58 aqueous humor (AH) samples from participants at the Veterans Administration (VA) Medical Center (Miami, FL). Patient samples used for 1H-Nuclear Magnetic Resonance (NMR) and Isotopic Ratio Outlier Analysis (IROA) consisted of individuals with POAG (n=23) and non-POAG controls (n=35).

Treatment:

Treatment ID:	TR001365
Treatment Summary:	No Treatment

Sample Preparation:

Sampleprep ID:	SP001358
Sampleprep Summary:	The 41 samples were prepared for isotopic ratio outlier analysis (IROA). Approximately 800 µL of precipitate solution (8:1:1 Acetonitrile: Methanol: Acetone) was added to the 50 µL of aqueous humor. The metabolites were vortexed and incubated at 4 °C for 30 minutes. This was followed by another incubation period at -20 °C for 1 hour. Each sample was centrifuged at 20,000 x g for 10 minutes at 4 °C (Beckman Microfuge 18) to form a pellet and 375 µL of supernatant was collected. The supernatant was dried in a speed vacuum for approximately 20 minutes or until the sample was fully dry and stored at -20 °C. The IROA internal standard (IROA-IS, IROA technologies) (U-95% 13C) was reconstituted in 1.2 mL of LC-MS grade water. The samples were reconstituted in 25 µL of LC-MS grade water and 10 µL was combined with 20 µL of IROA-IS and subjected to LC-MS/MS analysis. A long-term reference standard (LTRS) was reconstituted in 50 µL of LC-MS grade water and subjected to LC-MS/MS as the first, last, and every 10 samples. Metabolite identification and relative quantification were performed using Clusterfinder Build 3.1.10 (IROA Technologies).

Sampleprep ID:

SP001358

Sampleprep Summary:

The 41 samples were prepared for isotopic ratio outlier analysis (IROA). Approximately 800 µL of precipitate solution (8:1:1 Acetonitrile: Methanol: Acetone) was added to the 50 µL of aqueous humor. The metabolites were vortexed and incubated at 4 °C for 30 minutes. This was followed by another incubation period at -20 °C for 1 hour. Each sample was centrifuged at 20,000 x g for 10 minutes at 4 °C (Beckman Microfuge 18) to form a pellet and 375 µL of supernatant was collected. The supernatant was dried in a speed vacuum for approximately 20 minutes or until the sample was fully dry and stored at -20 °C. The IROA internal standard (IROA-IS, IROA technologies) (U-95% 13C) was reconstituted in 1.2 mL of LC-MS grade water. The samples were reconstituted in 25 µL of LC-MS grade water and 10 µL was combined with 20 µL of IROA-IS and subjected to LC-MS/MS analysis. A long-term reference standard (LTRS) was reconstituted in 50 µL of LC-MS grade water and subjected to LC-MS/MS as the first, last, and every 10 samples. Metabolite identification and relative quantification were performed using Clusterfinder Build 3.1.10 (IROA Technologies).

Combined analysis:

Analysis ID	AN002119
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Accela 600
Column	ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	UNSPECIFIED
Units	C12:C13 Ratio

Chromatography:

Chromatography ID:	CH001552
Instrument Name:	Thermo Accela 600
Column Name:	ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Column Temperature:	40 C
Flow Gradient:	s 0-40% solvent B over 10 minutes, 40% solvent B over 10-12 minutes, 60% solvent B over 12-14 minutes, 95% solvent B over 14-20 minutes,100% solvent B over 20-30 minutes
Flow Rate:	350 ul/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001974
Analysis ID:	AN002119
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Both Positive and Negative Ion Mode Metabolite identification and relative quantification were performed using Clusterfinder Build 3.1.10 (IROA Technologies). Thermo raw files were converted into mzxml files before importation into the Clusterfinder software. The manufacturer protocols were followed to recognize IROA peak pairs and determine molecular formulas. Metabolites were identified by comparing retention time, molecular formula and molecular ion m/z with the Mass Spectrometry Metabolite Library of Standards (MSMLS, IROA technologies).
Ion Mode:	UNSPECIFIED