Summary of Study ST001897
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 PR001193. The data can be accessed directly via it's Project DOI: 10.21228/M8H419 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.
| Study ID | ST001897 |
| Study Title | A local source of insulin in the eye governed by phagocytosis and starvation |
| Study Type | Untargeted Metabolomics |
| Study Summary | Untargeted metabolite analysis was performed on a Thermo Orbitrap IDX Tribrid MS to understand changes in metabolites in eye retina and RPE tissue during starvation. This study also probes the role of certain metabolites during phagocytosis. |
| Institute | University of Virginia |
| Department | Center of Cell Clearance , Microbiology, Immunology, and Cancer Biology |
| Laboratory | Kodi Ravichandraan Lab |
| Last Name | Etchegaray |
| First Name | Iker |
| Address | Center of Cell Clearance , Microbiology, Immunology, and Cancer Biology |
| kr4h@virginia.edu; jie3c@virginia.edu; nw5es@virginia.edu; | |
| Phone | 4023109931 |
| Submit Date | 2021-08-02 |
| Num Groups | 4 |
| Total Subjects | 2 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-12-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003078 | AN003079 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Orbitrap IDX | Orbitrap IDX |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | intensity | intensity |
MS:
| MS ID: | MS002863 |
| Analysis ID: | AN003078 |
| Instrument Name: | Orbitrap IDX |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Conventional DDA mode was used for data acquisition and samples were randomized during extraction and analysis on the mass spectrometer. The injection volume was 5 µL. ESI source condition were set as follows: Ion source type: H-ESI; positive ion voltage set at 3500 and negative at 2500. Sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was set at 275 °C while the vaporizer temperature was set at 320 °C. Data was acquired in full MS mode (1 µscan) at a resolution of 120,000 with a scan range of 67-1000 m/z at a normalized AGC Target of 25% and 50 millisecond of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 30,000. For data analysis, Thermo *.RAW files were converted to open source *.mzML format using msConvert software (http://proteowizard.sourceforge.net/download.html) and brought into MS-DIAL software for analysis (http://prime.psc.riken.jp/compms/msdial/main.html). MS-DIAL analysis parameters were as follows: MS1 tolerance was set at 0.01 Da and Ms2 tolerance at 0.025 Da. Data was collected from 0-15 min at a mass range from 50-1000 Da. Peak detection was performed with a minimum peak height of 1x105 and mass slice width of 0.1 Da. Metabolites were identified by searching the MS2 spectra in MS-DIAL public database (290,915 records for positive and 36,848 entries for negative mode; Version 14) using a mass tolerance of 0.01 Da for MS1 and 0.05 Da for MS/MS with identification score cutoff of 60%. Additionally, peaks were also searched against in-house IROA library (in both positive and negative mode) with a mass tolerance of 0.01, identification cutoff of 90% and RT tolerance of 0.5 min (Mass Spectrometry Metabolite Library of Standards (MSMLS); http://iroatech.com/). For peak alignment maximum retention tolerance was set at 0.2 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002864 |
| Analysis ID: | AN003079 |
| Instrument Name: | Orbitrap IDX |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Conventional DDA mode was used for data acquisition and samples were randomized during extraction and analysis on the mass spectrometer. The injection volume was 5 µL. ESI source condition were set as follows: Ion source type: H-ESI; positive ion voltage set at 3500 and negative at 2500. Sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was set at 275 °C while the vaporizer temperature was set at 320 °C. Data was acquired in full MS mode (1 µscan) at a resolution of 120,000 with a scan range of 67-1000 m/z at a normalized AGC Target of 25% and 50 millisecond of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 30,000. For data analysis, Thermo *.RAW files were converted to open source *.mzML format using msConvert software (http://proteowizard.sourceforge.net/download.html) and brought into MS-DIAL software for analysis (http://prime.psc.riken.jp/compms/msdial/main.html). MS-DIAL analysis parameters were as follows: MS1 tolerance was set at 0.01 Da and Ms2 tolerance at 0.025 Da. Data was collected from 0-15 min at a mass range from 50-1000 Da. Peak detection was performed with a minimum peak height of 1x105 and mass slice width of 0.1 Da. Metabolites were identified by searching the MS2 spectra in MS-DIAL public database (290,915 records for positive and 36,848 entries for negative mode; Version 14) using a mass tolerance of 0.01 Da for MS1 and 0.05 Da for MS/MS with identification score cutoff of 60%. Additionally, peaks were also searched against in-house IROA library (in both positive and negative mode) with a mass tolerance of 0.01, identification cutoff of 90% and RT tolerance of 0.5 min (Mass Spectrometry Metabolite Library of Standards (MSMLS); http://iroatech.com/). For peak alignment maximum retention tolerance was set at 0.2 min. |
| Ion Mode: | NEGATIVE |
