Summary of Study ST003075
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 PR001915. The data can be accessed directly via it's Project DOI: 10.21228/M86137 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 | ST003075 |
| Study Title | HZV029 TwoPhase Metabolomics and Lipidomics |
| Study Summary | In this study, a subset of plasma samples were processed using an in-house two phase extraction protocol based on the protocol originally proposed by Matayash et al. The resulting non-polar layer was then analyzed on a Thermo ScientificTM TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization source. This dataset was collected as a single batch and was used for the pipeline's ability to detect failed injections, which in this study, was simulated through the substitution of an empty vial for a missing study sample. |
| Institute | Jackson Laboratory for Genomic Medicine |
| Laboratory | Shuzhao Li Laboratory |
| Last Name | Joshua |
| First Name | Mitchell |
| Address | 10 Discovery Dr, Farmington CT 06032 |
| joshua.mitchell@jax.org | |
| Phone | 8608372474 |
| Submit Date | 2024-02-15 |
| Publications | Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li doi: https://doi.org/10.1101/2024.02.13.580048 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005033 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Accucore HILIC (100 x 2.1mm,2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid |
| Ion Mode | NEGATIVE |
| Units | peak intensity |
Chromatography:
| Chromatography ID: | CH003804 |
| Chromatography Summary: | The chromatographic separations were performed using Thermo ScientificTM TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization source, using both positive and negative ionization mode with a run time of 8.5 min for polar and 12 min for non-polar extract. All samples were maintained at 4 °C in the autosampler. Data were acquired for polar and non-polar extract using HILIC, respectively in full scan mode with mass resolution of 60,000. An AccucoreTM-150-Amide HILIC column (2.6 mm, 2.1 mm x 100 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) was used for polar extract. 10 mM ammonium acetate in acetonitrile:water (95:5, v/v) with 0.1% acetic acid as mobile phase A and 10 mM ammonium acetate in acetonitrile:water (50:50, v/v) with 0.1% acetic acid as mobile phase B were used for HILIC method. For HILIC acquisition, following gradient was applied at a flow rate of 0.55 ml/min: 0-0.2 min: 0% B, 0.20-8.75 min: 98% B, and 11.25 min for cleaning and equilibration of column. Mass spectrometry data were collected with the following MS settings: mass range, 100-1700 m/z for lipidomics and 60-1000 for metabolomics; spray voltage, 3200 V (ESI+), 2800 V (ESI-); sheath gas, 45 Arb; auxiliary gas, 20 Arb; sweep gas, 1 Arb; ion transfer tube temperature, 325 °C; vaporizer temperature, 325 °C; full scan mass resolution, 60,000 (MS1); normalized AGC target (%), 25; maximum injection time, 100 ms. Data dependent fragmentation (dd-MS/MS) parameters for each polarity as follows: isolation window (m/z), 1.2; stepped HCD collision energy (%), 20,40,80; dd-MS/MS resolution, 30,000; normalized AGC target (%), 20; maximum injection time (ms), 54; micro scan, 1; cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to collect MS2 spectra for identification of compounds. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore HILIC (100 x 2.1mm,2.6um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.2 min: 0% B, 0.20-8.75 min: 98% B, and 11.25 min for cleaning and equilibration of column |
| Flow Rate: | 0.55 ml/min |
| Solvent A: | 95% acetonitrile/5% water; 0.1% acetic acid; 10 mM ammonium acetate |
| Solvent B: | 50% acetonitrile/50% water; 0.1% acetic acid; 10 mM ammonium acetate |
| Chromatography Type: | HILIC |
