Summary of Study ST002233
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 PR001423. The data can be accessed directly via it's Project DOI: 10.21228/M8SD86 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 | ST002233 |
| Study Title | Batch variation of large scale LC-MS metabolomics analysis of human plasma samples |
| Study Summary | Metabolomics holds the promise to measure and quantify small molecules comprehensively in biological systems, and LC-MS (liquid chromatography coupled mass spectrometry) has become the leading technology in the field. Significant challenges still exist in the computational processing of data from LC-MS metabolomic experiments into metabolite features, including provenance and reproducibility of the current software tools. Current dataset, named HZV029, comprises of 268 data files, from two QC (human pooled plasma) samples that were analyzed repeatedly over 17 batches, on a Thermo Scientific Orbitrap ID-X Tribrid mass spectrometer, coupled with dual liquid chromatography via a Transcend LX-2 System. It provides a unique opportunity to be used as a benchmark dataset to evaluate reproducibility via available choices of different processing tools without knowing the ground truth about these QC samples. |
| Institute | The Jackson Laboratory for Genomic Medicine |
| Laboratory | Shuzhao Li Lab |
| Last Name | Siddiqa |
| First Name | Amnah |
| Address | 10 Discovery Drive , Farmington, CT 06032 |
| amnah.siddiqa@jax.org | |
| Phone | 404-918 7223 |
| Submit Date | 2022-04-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-11-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003643 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Scientific Vanquish Horizon UHPLC system |
| Column | HILIC column, AccucoreTM-150-Amide (50 x 2.1mm,2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid |
| Ion Mode | POSITIVE |
| Units | m/z values |
Chromatography:
| Chromatography ID: | CH002697 |
| Chromatography Summary: | Mobile phase: 10 mM ammonium acetate in 95% acetonitrile containing 0.1% acetic acid as mobile phase A and 10 mM ammonium acetate in 50% acetonitrile containing 0.1% acetic acid as mobile phase B were used for HILIC method. Mobile phase gradient: 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, 5.00-5.50 min: 0% B and 4.5 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, 5.00-5.10 min: 0% B and 4.9 min cleaning and column equilibration. |
| Instrument Name: | Thermo Scientific Vanquish Horizon UHPLC system |
| Column Name: | HILIC column, AccucoreTM-150-Amide (50 x 2.1mm,2.6um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.1 min: 0% B, 0.10-5.0 min: 98% B, 5.00-5.50 min: 0% B and 4.5 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 |
