Summary of Study ST000624
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 PR000450. The data can be accessed directly via it's Project DOI: 10.21228/M8WC8S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000624 |
| Study Title | Human trabecular meshowrk phospholipid profiles of control and glaucomatous eyes |
| Study Summary | We compared phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol) profiles of control and glaucomatous trabecular meshwork (TM) derived from human donors.Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford method, and for select samples confirmed with densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ quantum Access Max triple quadrupole mass spectrometer with precursor ion scan (PIS) or neutral ion loss scan (NLS), using appropriate class specific lipid standards. |
| Institute | University of Miami |
| Last Name | Bhattacharya |
| First Name | Sanjoy |
| Address | McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136 |
| SBhattacharya@med.miami.edu | |
| Phone | 305-482-4103 |
| Submit Date | 2017-06-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | MS(Dir. Inf.) |
| Release Date | 2019-07-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000450 |
| Project DOI: | doi: 10.21228/M8WC8S |
| Project Title: | Phospholipid Profiling of Human Glaucomatous and Control Aqueous Humor and Trabecular Meshwork |
| Project Summary: | In this study we used a triple quadrupole mass spectrometer to investigate the phospholipids within human aqueous humor and trabecular meshwork. Our aim was to find potential differences in the lipid profiles between control and glaucomatous donors to better understand the disease. |
| Institute: | University of Miami |
| Last Name: | Bhattacharya |
| First Name: | Sanjoy |
| Address: | 1638 NW 10th Avenue, Miami, Florida, 33136, USA |
| Email: | sbhattacharya@med.miami.edu |
| Phone: | 3054824103 |
Subject:
| Subject ID: | SU000647 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition |
|---|---|---|
| SA035092 | NTM16L1 | Control |
| SA035093 | NTM14L1 | Control |
| SA035094 | NTM13L1 | Control |
| SA035095 | NTM17L1 | Control |
| SA035096 | NTM19L1 | Control |
| SA035097 | NTM1L1 | Control |
| SA035098 | NTM20L1 | Control |
| SA035099 | NTM12L1 | Control |
| SA035100 | NTM18L1 | Control |
| SA035101 | NTM15L1 | Control |
| SA035102 | NTM5L1 | Control |
| SA035103 | NTM4L1 | Control |
| SA035104 | NTM11L1 | Control |
| SA035105 | NTM2L1 | Control |
| SA035106 | NTM6L1 | Control |
| SA035107 | NTM3L1 | Control |
| SA035108 | NTM7L1 | Control |
| SA035109 | NTM10L1 | Control |
| SA035110 | NTM9L1 | Control |
| SA035111 | NTM8L1 | Control |
| SA035112 | GTM15L1 | Glaucomatous |
| SA035113 | GTM14L1 | Glaucomatous |
| SA035114 | GTM13L1 | Glaucomatous |
| SA035115 | GTM16L1 | Glaucomatous |
| SA035116 | GTM19L1 | Glaucomatous |
| SA035117 | GTM12L1 | Glaucomatous |
| SA035118 | GTM20L1 | Glaucomatous |
| SA035119 | GTM18L1 | Glaucomatous |
| SA035120 | GTM17L1 | Glaucomatous |
| SA035121 | GTM1L1 | Glaucomatous |
| SA035122 | GTM5L1 | Glaucomatous |
| SA035123 | GTM4L1 | Glaucomatous |
| SA035124 | GTM3L1 | Glaucomatous |
| SA035125 | GTM2L1 | Glaucomatous |
| SA035126 | GTM6L1 | Glaucomatous |
| SA035127 | GTM7L1 | Glaucomatous |
| SA035128 | GTM10L1 | Glaucomatous |
| SA035129 | GTM9L1 | Glaucomatous |
| SA035130 | GTM8L1 | Glaucomatous |
| SA035131 | GTM11L1 | Glaucomatous |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO000641 |
| Collection Summary: | Donor tissues were used following the institutional review board approved protocols and adhering to the tenets of the Declaration of Helsinki. Control TM and a subset of primary open-angle glaucoma (POAG) TM were collected from cadaver donors, a limited subset of POAG surgical specimen (acquired under institutional review board approved/exempted protocols) also were used for these studies. Cadaver donor tissues were sourced from Midwest Eye-Banks, Lions Eye Bank (Miami, FL), National Disease Research Interchange (NDRI; Philadelphia, PA), and Mundorf Eye Institute (Charlotte, NC). The postmortem time ranged from 3 to 16 hours. Control TM was stored briefly in Optisol at 48 and then used for lipid extraction. POAG TM tissues were stored at -80˚C until time of use. The mean age of control donors was 58.2 +/- 13.7 years and the mean age of glaucomatous TM donors 66 +/- 9.5 years. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR000661 |
| Treatment Summary: | No treament was performed on tissue. |
Sample Preparation:
| Sampleprep ID: | SP000654 |
| Sampleprep Summary: | Isolated trabecular meshwork tissue was subjected to an alternating cycle of immersion in liquid nitrogen and 37˚C, followed by extraction of lipids using a modified Bligh and Dryer method.13 The organic phase with extracted lipids was dried in a Speed-Vac (Model 7810014; Labconco, Kansas City, MO). Samples were flushed with argon gas to prevent oxidation. Corresponding aqueous phase extracted proteins were subjected to determination of concentration using Bradford’s method. A subset of protein samples also were subjected to densitometric quantification using bovine serum albumin as a standard (amino acid quantified) after electrophoretic separation on a PHAST (GE Healthcare Bio-Sciences AB, Uppsala, Sweden) gel system. All extractions and subsequent handling were made using glass vials, and polyvinyl plastic was avoided completely. We also added a PC control standard during tissue homogenization, determined its recovery in an aliquot, and used for the calculation of total recovery of this standard for each extraction to ensure >99% recovery of added standard during extraction. |
Combined analysis:
| Analysis ID | AN000956 |
|---|---|
| Analysis type | MS |
| Chromatography type | None (Direct infusion) |
| Chromatography system | None |
| Column | none |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Thermo Quantiva Access Max |
| Ion Mode | UNSPECIFIED |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH000681 |
| Instrument Name: | None |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS000851 |
| Analysis ID: | AN000956 |
| Instrument Name: | Thermo Quantiva Access Max |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | UNSPECIFIED |
