Summary of Study ST003109
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 | ST003109 |
| Study Title | HZV029 Metabolomics |
| Study Summary | In this study, plasma samples were processed using an in-house one phase extraction protocol as previously published (Siddiqa, A., et al., A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination. npj Vaccines, 2023. 8(1): p. 92. ). The resulting extract 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 over 17 batches and was used to evaluate the QA/QC metrics produced by the pipeline and resulting MS2 annotations generated from a complimentary AcquireX (deep scan) MS2 dataset were compared to compound discoverer. |
| 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 | AN005091 | AN005092 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore HILIC (100 x 2.1mm,2.6um) | Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid | Thermo Orbitrap ID-X tribrid |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak intensity | peak intensity |
Chromatography:
| Chromatography ID: | CH003847 |
| 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 positive and negative ionization modes. All samples were maintained at 4 °C in the autosampler. Data were acquired using hydrophilic interaction liquid chromatography (HILIC) and reversed phase (RP) column in parallel both in positive and negative polarities in full scan mode with mass resolution of 120,000. An AccucoreTM−150-Amide HILIC column (2.6 μm, 2.1 mm × 50 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) and a Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) embedded with Hypersil GOLDTM RP guard column (2.1 mm x 10 mm, 3 μm) (Thermo Fisher Scientific, MA, USA. Cat. 25003-012101) maintained at 45 °C were used for chromatographic separation. 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. 0.1% formic acid in water and 0.1% formic acid in acetonitrile were used as mobile phase A and B respectively for RP acquisition. For HILIC acquisition, following gradient was applied at a flow rate of 0.55 ml/min: 0–0.1 min: 0% B, 0.10–5.0 min: 98% B, and 5 min for cleaning and equilibration of column. For RP column, following gradient was applied at a flow rate of 0.4 ml/min: 0–0.1 min: 0% B, 0.10–1.9 min: 60% B, 1.9–5.0 min: 98% B, and 5 min cleaning and column equilibration. This way the mass spec data for each sample was collected consecutively, carrying only one (either HILIC or RP) eluent to the MS for 5 min, while the other eluent was directed to the waste during washing and re-equilibration. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore HILIC (100 x 2.1mm,2.6um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0–0.1 min: 0% B, 0.10–5.0 min: 98% B, and 5 min for cleaning and equilibration of column |
| Flow Rate: | 0.55 ml/min |
| Solvent A: | 95% acetonitrile/5% water; 10 mM ammonium acetate; 0.1% acetic acid |
| Solvent B: | 50% acetonitrile/50% water; 10 mM ammonium acetate; 0.1% acetic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003848 |
| 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 positive and negative ionization modes. All samples were maintained at 4 °C in the autosampler. Data were acquired using hydrophilic interaction liquid chromatography (HILIC) and reversed phase (RP) column in parallel both in positive and negative polarities in full scan mode with mass resolution of 120,000. An AccucoreTM−150-Amide HILIC column (2.6 μm, 2.1 mm × 50 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) and a Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) embedded with Hypersil GOLDTM RP guard column (2.1 mm x 10 mm, 3 μm) (Thermo Fisher Scientific, MA, USA. Cat. 25003-012101) maintained at 45 °C were used for chromatographic separation. 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. 0.1% formic acid in water and 0.1% formic acid in acetonitrile were used as mobile phase A and B respectively for RP acquisition. For HILIC acquisition, following gradient was applied at a flow rate of 0.55 ml/min: 0–0.1 min: 0% B, 0.10–5.0 min: 98% B, and 5 min for cleaning and equilibration of column. For RP column, following gradient was applied at a flow rate of 0.4 ml/min: 0–0.1 min: 0% B, 0.10–1.9 min: 60% B, 1.9–5.0 min: 98% B, and 5 min cleaning and column equilibration. This way the mass spec data for each sample was collected consecutively, carrying only one (either HILIC or RP) eluent to the MS for 5 min, while the other eluent was directed to the waste during washing and re-equilibration. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) |
| Column Temperature: | 45 |
| Flow Gradient: | 0–0.1 min: 0% B, 0.10–1.9 min: 60% B, 1.9–5.0 min: 98% B, and 5 min cleaning and column equilibration |
| Flow Rate: | 0.4 ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
