Summary of Study ST002399
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 PR001533. The data can be accessed directly via it's Project DOI: 10.21228/M8J99C 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 | ST002399 |
| Study Title | Metabolomics of Adipocyte-Conditioned Media Compared to Stromal Cell- and Un-conditioned Media |
| Study Type | Untargeted MS |
| Study Summary | The metabolomics profiles of adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were analyzed by untargeted mass spectrometry. |
| Institute | Emory University |
| Department | Pediatrics |
| Laboratory | Joshua Chandler, PhD |
| Last Name | Chandler |
| First Name | Joshua |
| Address | 2015 Uppergate Drive NE, Atlanta, GA 30322 |
| joshua.chandler@emory.edu | |
| Phone | 404-727-3536 |
| Submit Date | 2022-10-21 |
| Num Groups | 3 (ACM vs SCM vs UCM) |
| Total Subjects | 5 replicates of each group (15 total) |
| Publications | submitted to JNCI |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003906 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | Peak area |
MS:
| MS ID: | MS003645 |
| Analysis ID: | AN003906 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Compound Discoverer 3.3 (Thermo Scientific) was used for data analysis of metabolomic experiments, including retention time alignment across runs, cubic spline normalization of areas for each metabolite in quality control pooled samples, and gap-filling based on real peak detection. The minimum peak intensity was 5x105, and metabolites were excluded if they had >50% relative standard deviation after correction or a max sample area <5-fold that of the blank. Furthermore, to be considered a high-confidence metabolite for analysis, metabolites required a) an accurate mass (5 ppm) match and either (i) retention time (±5%) matching of reference standards, and/or (ii) matching to MS2 spectra in mzCloud (mzcloud.org) (including at least one matching product ion); b) an accurate mass and retention time match to a lipid identity determined by LipidSearch (ThermoFisher, all default parameters used) based on MS2 data; and/or c) an MS2 fragment ion matching to a particular class of compounds (184.1 for phosphatidylcholine). When a chromatographic peak matched to two standards of similar retention time that were indistinguishable by MS2, we prioritized the metabolite with higher abundance in human or retained both annotations. The naming convention for the metabolites reported herein is as follows – a) if the metabolite was an accurate mass and retention time match to our curated library or to our LipidSearch library, it is listed only as the metabolite name; b) if the metabolite had an MS2 library match but no match in the aforementioned libraries, it is listed as the MS2 match and the retention time; c) if the metabolite had an MS2 compound class match, it is listed as the compound class, the chemical formula (or the molecular weight if formula was not available), and the retention time. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 |
| Ionization Potential: | +3.5 kV |
| Automatic Gain Control: | 1E6 |
