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:
Project:
| Project ID: | PR001193 |
| Project DOI: | doi: 10.21228/M8H419 |
| Project Title: | Untargeted metabolomics to understand metabolism of local source of insulin in the eye governed by phagocytosis and starvation |
| Project Type: | Untargeted Metabolomics (UPLC-MS/MS) |
| Project 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: | Department of Microbiology, Immunology, and Cancer Biology, University of Virginia |
| Email: | jie3c@virginia.edu; kr4h@virginia.edu; nw5es@virginia.edu |
| Phone: | 4023109931 |
Subject:
| Subject ID: | SU001975 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | group |
|---|---|---|
| SA176068 | Sample_p_007 | KO_Retina |
| SA176069 | Sample_n_019 | KO_Retina |
| SA176070 | Sample_n_003 | KO_Retina |
| SA176071 | Sample_p_003 | KO_Retina |
| SA176072 | Sample_p_015 | KO_Retina |
| SA176073 | Sample_n_011 | KO_Retina |
| SA176074 | Sample_p_019 | KO_Retina |
| SA176075 | Sample_p_011 | KO_Retina |
| SA176076 | Sample_n_015 | KO_Retina |
| SA176077 | Sample_n_007 | KO_Retina |
| SA176058 | Sample_n_016 | KO_RPE |
| SA176059 | Sample_p_020 | KO_RPE |
| SA176060 | Sample_p_008 | KO_RPE |
| SA176061 | Sample_p_004 | KO_RPE |
| SA176062 | Sample_n_020 | KO_RPE |
| SA176063 | Sample_p_012 | KO_RPE |
| SA176064 | Sample_n_012 | KO_RPE |
| SA176065 | Sample_n_004 | KO_RPE |
| SA176066 | Sample_p_016 | KO_RPE |
| SA176067 | Sample_n_008 | KO_RPE |
| SA176078 | Sample_p_QC2 | QC |
| SA176079 | Sample_n_QC5 | QC |
| SA176080 | Sample_p_QC1 | QC |
| SA176081 | Sample_n_QC1 | QC |
| SA176082 | Sample_p_QC4 | QC |
| SA176083 | Sample_p_QC5 | QC |
| SA176084 | Sample_n_QC4 | QC |
| SA176085 | Sample_p_QC3 | QC |
| SA176086 | Sample_n_QC3 | QC |
| SA176087 | Sample_n_QC2 | QC |
| SA176098 | Sample_p_001 | WT_Retina |
| SA176099 | Sample_n_013 | WT_Retina |
| SA176100 | Sample_n_009 | WT_Retina |
| SA176101 | Sample_n_005 | WT_Retina |
| SA176102 | Sample_n_017 | WT_Retina |
| SA176103 | Sample_n_001 | WT_Retina |
| SA176104 | Sample_p_013 | WT_Retina |
| SA176105 | Sample_p_009 | WT_Retina |
| SA176106 | Sample_p_005 | WT_Retina |
| SA176107 | Sample_p_017 | WT_Retina |
| SA176088 | Sample_n_002 | WT_RPE |
| SA176089 | Sample_p_002 | WT_RPE |
| SA176090 | Sample_p_014 | WT_RPE |
| SA176091 | Sample_n_010 | WT_RPE |
| SA176092 | Sample_n_006 | WT_RPE |
| SA176093 | Sample_p_010 | WT_RPE |
| SA176094 | Sample_p_006 | WT_RPE |
| SA176095 | Sample_n_018 | WT_RPE |
| SA176096 | Sample_n_014 | WT_RPE |
| SA176097 | Sample_p_018 | WT_RPE |
| Showing results 1 to 50 of 50 |
Collection:
| Collection ID: | CO001968 |
| Collection Summary: | Overnight fasted mice were euthanized with avertin after light onset. Five replicates each of both Retinal and RPE tissues (from wild type and knock out mice) were harvested/dissected, flash frozen and stored in -80 ºC until extraction. Tissues were thawed on ice and extracted using methanol:chloroform (2:1) at 4C and phase separated using water. Top aq. phase was recovered as metabolite mixture and dried overnight in speedVac and reconstituted in 100 µL of 0.1% Formic acid in water. Ten µl from each tube was removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 5 sample injection. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR001987 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP001981 |
| Sampleprep Summary: | Overnight fasted mice were euthanized with avertin after light onset. Five replicates each of both Retinal and RPE tissues (from wild type and knock out mice) were harvested/dissected, flash frozen and stored in -80 ºC until extraction. Tissues were thawed on ice and extracted using methanol:chloroform (2:1) at 4C and phase separated using water. Top aq. phase was recovered as metabolite mixture and dried overnight in speedVac and reconstituted in 100 µL of 0.1% Formic acid in water. Ten µl from each tube was removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 5 sample injection. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
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 |
Chromatography:
| Chromatography ID: | CH002276 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 30C |
| Flow Gradient: | 0-8 minutes 50% B, 8 – 13 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
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 |
