Summary of Study ST002233

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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.

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Study IDST002233
Study TitleBatch variation of large scale LC-MS metabolomics analysis of human plasma samples
Study SummaryMetabolomics 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.
The Jackson Laboratory for Genomic Medicine
LaboratoryShuzhao Li Lab
Last NameSiddiqa
First NameAmnah
Address10 Discovery Drive , Farmington, CT 06032
Phone404-918 7223
Submit Date2022-04-11
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-11-01
Release Version1
Amnah Siddiqa Amnah Siddiqa application/zip

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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 instrument type Orbitrap
MS instrument name Thermo Orbitrap ID-X tribrid
Units m/z values


MS ID:MS003394
Analysis ID:AN003643
Instrument Name:Thermo Orbitrap ID-X tribrid
Instrument Type:Orbitrap
MS Comments:None