Summary of Study ST000616
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 | ST000616 |
| Study Title | Human Aqueous Humor Phospholipids in Control and Glaucomatous eyes |
| Study Summary | An analysis of phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine and phosphatidylinositol) classes in human control and glaucomatous aqueous humor (AH). Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford’s method, and select samples were confirmed with Densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ Quantum Access Max triple quadrupole mass spectrometer utilizing precursor ion scan (PIS) or neutral ion loss scan (NLS) using appropriate class specific lipid standards in a two-step quantification process. Mass spectrometer data were analyzed using MzMine 2.23. |
| Institute | University of Miami |
| Last Name | Bhattacharya |
| First Name | Sanjoy |
| Address | 1638 NW 10th Avenue, Miami, Florida, 33136, USA |
| sbhattacharya@med.miami.edu | |
| Phone | 3054824103 |
| Submit Date | 2017-05-31 |
| 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: | SU000639 |
| 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 |
|---|---|---|
| SA034156 | NAH16L1 | Control |
| SA034157 | NAH14L1 | Control |
| SA034158 | NAH13L1 | Control |
| SA034159 | NAH17L1 | Control |
| SA034160 | NAH19L1 | Control |
| SA034161 | NAH1BL1 | Control |
| SA034162 | NAH20L1 | Control |
| SA034163 | NAH12L1 | Control |
| SA034164 | NAH18L1 | Control |
| SA034165 | NAH15L1 | Control |
| SA034166 | NAH5BL1 | Control |
| SA034167 | NAH4BL1 | Control |
| SA034168 | NAH11L1 | Control |
| SA034169 | NAH2BL1 | Control |
| SA034170 | NAH6BL1 | Control |
| SA034171 | NAH3BL1 | Control |
| SA034172 | NAH7BL1 | Control |
| SA034173 | NAH10BL1 | Control |
| SA034174 | NAH9BL1 | Control |
| SA034175 | NAH8BL1 | Control |
| SA034176 | GAH15L1 | Glaucomatous |
| SA034177 | GAH14L1 | Glaucomatous |
| SA034178 | GAH13L1 | Glaucomatous |
| SA034179 | GAH16L1 | Glaucomatous |
| SA034180 | GAH19L1 | Glaucomatous |
| SA034181 | GAH12L1 | Glaucomatous |
| SA034182 | GAH20L1 | Glaucomatous |
| SA034183 | GAH18L1 | Glaucomatous |
| SA034184 | GAH17L1 | Glaucomatous |
| SA034185 | GAH1BL1 | Glaucomatous |
| SA034186 | GAH5BL1 | Glaucomatous |
| SA034187 | GAH4BL1 | Glaucomatous |
| SA034188 | GAH3BL1 | Glaucomatous |
| SA034189 | GAH2BL1 | Glaucomatous |
| SA034190 | GAH6BL1 | Glaucomatous |
| SA034191 | GAH7BL1 | Glaucomatous |
| SA034192 | GAH10BL1 | Glaucomatous |
| SA034193 | GAH9BL1 | Glaucomatous |
| SA034194 | GAH8BL1 | Glaucomatous |
| SA034195 | GAH11L1 | Glaucomatous |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO000633 |
| Collection Summary: | Control and POAG AH were procured during glaucoma, cataract surgeries following institutional review board approved protocols, and principles outlined in the Declaration of Helsinki were adhered to. A total of 20 control and 20 glaucomatous AH samples were included for these studies. All AH samples were immediately stored at −80°C until time of use. The mean age of donors was 69.5 ± 9.9 years and both genders were included for these studies. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR000653 |
| Treatment Summary: | No treatment was performed on the eyes. |
Sample Preparation:
| Sampleprep ID: | SP000646 |
| Sampleprep Summary: | Aqueous humor samples were subjected to extraction of lipids using suitable and minimal modification of Bligh and Dyer method. The lower organic phase containing the extracted lipids was isolated and solvent dried with a Speed-Vac (Model 7810014; Labconco, Kansas City, MO). Samples were subsequently flushed with argon gas to prevent oxidation. Proteins recovered from the corresponding upper aqueous phase were quantified using the Bradford method. A subset of protein samples were also subjected to densitometric quantification using bovine serum albumin (BSA) as a standard (amino acid quantified) after electrophoretic separation on a PHAST (GE Healthcare Bio-Sciences AB, Sweden) gel system. We repeated protein estimations using an amino acid analyzer after overnight digestion in hydrochloric acid following previously published protocols. The protein amounts determined using amino acid analyzer were utilized in normalization of lipids per amount of proteins. In order to determine and ensure extraction efficiency, ovine wool cholesterol (molecular mass 386.7; catalog no. 700000; Avanti Polar Lipids, Albaster, AL) was premixed with AH prior to extraction. All extractions and subsequent handling were made using glass vials to avoid contaminating impurities. The quantification lipid standards (all procured from Avanti Polar Lipids, Albaster, AL) we used were ditridecanoyl-sn-glycero-3-phosphocholine (molecular mass 649.89, catalog no. 850340) for PCs, 1,2-dioleoyl-snglycero- 3-phospho-L-serine (molecular mass 810.03, catalog no. 840035) for PSs, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (molecular mass 744.04, catalog no. 850725) for PEs and 1,2-dioleoyl-sn-glycero-3-phospho-(10-myo-inositol) (molecular mass 880.15, catalog no. 850149) for PIs. |
Combined analysis:
| Analysis ID | AN000945 |
|---|---|
| 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: | CH000673 |
| Instrument Name: | None |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS000841 |
| Analysis ID: | AN000945 |
| Instrument Name: | Thermo Quantiva Access Max |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | UNSPECIFIED |
