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 |
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Sample Preparation:
| Sampleprep ID: | SP002325 |
| Sampleprep Summary: | The plasma samples were thawed in ice. Metabolites extraction were carried out by protein precipitation using extraction solvent, acetonitrile:methanol (8:1, v/v) containing 0.1% formic acid and isotope labelled Trimethyl-13C3]-caffeine, [13C5]-L-glutamic acid, [15N2]-Uracil, [15N,13C5]-L-methionine, [13C6]-D-glucose and [15N]-L-tyrosin as spike-in controls. 30 μl of plasma was taken and 60 μl of extraction solvent was added. All samples were vortexed and incubated with shaking at 1000 rpm for 10 min at 4°C followed by centrifugation at 4°C for 15 min at 15,000 rpm. The supernatant was transferred into mass spec vials and 2 μl injected into UHPLC-MS. |
| Extraction Method: | Protein precipitation |
| Extract Storage: | -80℃ |
