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.

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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.
Institute
The Jackson Laboratory for Genomic Medicine
LaboratoryShuzhao Li Lab
Last NameSiddiqa
First NameAmnah
Address10 Discovery Drive , Farmington, CT 06032
Emailamnah.siddiqa@jax.org
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
https://dx.doi.org/10.21228/M8SD86
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001423
Project DOI:doi: 10.21228/M8SD86
Project Title:Batch variation of large scale LC-MS metabolomics analysis of human plasma samples
Project 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
Email:amnah.siddiqa@jax.org
Phone:404-918 7223
Funding Source:1R01AI149746 (NIH-NIAID)

Subject:

Subject ID:SU002319
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id SampleType
SA212663batch17_MT_20210811_001GCommercialQstdPooled
SA212664batch17_MT_20210811_001ECommercialQstdPooled
SA212665batch17_MT_20210811_089CommercialQstdPooled
SA212666batch17_MT_20210811_187CommercialQstdPooled
SA212667batch17_MT_20210811_189CommercialQstdPooled
SA212668batch17_MT_20210811_001KCommercialQstdPooled
SA212669batch17_MT_20210811_001ICommercialQstdPooled
SA212670batch17_MT_20210811_087CommercialQstdPooled
SA212671batch17_MT_20210811_001CCommercialQstdPooled
SA212672batch16_MT_20210810_001ICommercialQstdPooled
SA212673batch16_MT_20210810_193CommercialQstdPooled
SA212674batch16_MT_20210810_001KCommercialQstdPooled
SA212675batch17_MT_20210811_001CommercialQstdPooled
SA212676batch17_MT_20210811_001ACommercialQstdPooled
SA212677batch17_MT_20210811_003CommercialQstdPooled
SA212678batch2_MT_20210727_001CommercialQstdPooled
SA212679batch2_MT_20210727_087CommercialQstdPooled
SA212680batch4_MT_20210729_001CommercialQstdPooled
SA212681batch3_MT_20210728_189CommercialQstdPooled
SA212682batch3_MT_20210728_187CommercialQstdPooled
SA212683batch4_MT_20210729_003CommercialQstdPooled
SA212684batch4_MT_20210729_001ACommercialQstdPooled
SA212685batch4_MT_20210729_087CommercialQstdPooled
SA212686batch4_MT_20210729_003CCommercialQstdPooled
SA212687batch3_MT_20210728_089CommercialQstdPooled
SA212688batch3_MT_20210728_087CommercialQstdPooled
SA212689batch2_MT_20210727_089CommercialQstdPooled
SA212690batch16_MT_20210810_191CommercialQstdPooled
SA212691batch2_MT_20210727_177CommercialQstdPooled
SA212692batch2_MT_20210727_179CommercialQstdPooled
SA212693batch3_MT_20210728_003CommercialQstdPooled
SA212694batch3_MT_20210728_001CommercialQstdPooled
SA212695batch2_MT_20210727_003CommercialQstdPooled
SA212696batch16_MT_20210810_001GCommercialQstdPooled
SA212697batch14_MT_20210808_001ICommercialQstdPooled
SA212698batch14_MT_20210808_181CommercialQstdPooled
SA212699batch14_MT_20210808_179CommercialQstdPooled
SA212700batch14_MT_20210808_001KCommercialQstdPooled
SA212701batch15_MT_20210809_001CommercialQstdPooled
SA212702batch15_MT_20210809_001ACommercialQstdPooled
SA212703batch15_MT_20210809_003CommercialQstdPooled
SA212704batch14_MT_20210808_001GCommercialQstdPooled
SA212705batch14_MT_20210808_001ECommercialQstdPooled
SA212706batch14_MT_20210808_003CommercialQstdPooled
SA212707batch14_MT_20210808_001CommercialQstdPooled
SA212708batch14_MT_20210808_001ACommercialQstdPooled
SA212709batch14_MT_20210808_001CCommercialQstdPooled
SA212710batch14_MT_20210808_089CommercialQstdPooled
SA212711batch14_MT_20210808_087CommercialQstdPooled
SA212712batch15_MT_20210809_001CCommercialQstdPooled
SA212713batch15_MT_20210809_087CommercialQstdPooled
SA212714batch16_MT_20210810_001A_20210809142420CommercialQstdPooled
SA212715batch16_MT_20210810_003_20210809141340CommercialQstdPooled
SA212716batch16_MT_20210810_001C_20210809143500CommercialQstdPooled
SA212717batch16_MT_20210810_087CommercialQstdPooled
SA212718batch16_MT_20210810_001ECommercialQstdPooled
SA212719batch16_MT_20210810_089CommercialQstdPooled
SA212720batch16_MT_20210810_001_20210809140300CommercialQstdPooled
SA212721batch15_MT_20210809_001KCommercialQstdPooled
SA212722batch15_MT_20210809_001ECommercialQstdPooled
SA212723batch15_MT_20210809_089CommercialQstdPooled
SA212724batch15_MT_20210809_001GCommercialQstdPooled
SA212725batch15_MT_20210809_187CommercialQstdPooled
SA212726batch15_MT_20210809_001ICommercialQstdPooled
SA212727batch15_MT_20210809_189CommercialQstdPooled
SA212728batch4_MT_20210729_089CommercialQstdPooled
SA212729batch4_MT_20210729_003GCommercialQstdPooled
SA212730batch8_MT_20210802_001ACommercialQstdPooled
SA212731batch8_MT_20210802_003CommercialQstdPooled
SA212732batch8_MT_20210802_001CommercialQstdPooled
SA212733batch8_MT_20210802_003CCommercialQstdPooled
SA212734batch8_MT_20210802_087CommercialQstdPooled
SA212735batch8_MT_20210802_001ECommercialQstdPooled
SA212736batch8_MT_20210802_089CommercialQstdPooled
SA212737batch7_MT_20210801_003KCommercialQstdPooled
SA212738batch7_MT_20210801_001ICommercialQstdPooled
SA212739batch7_MT_20210801_089CommercialQstdPooled
SA212740batch7_MT_20210801_087CommercialQstdPooled
SA212741batch7_MT_20210801_001ECommercialQstdPooled
SA212742batch7_MT_20210801_003GCommercialQstdPooled
SA212743batch7_MT_20210801_183CommercialQstdPooled
SA212744batch7_MT_20210801_181CommercialQstdPooled
SA212745batch8_MT_20210802_003GCommercialQstdPooled
SA212746batch8_MT_20210802_189CommercialQstdPooled
SA212747batch9_MT_20210803_003GCommercialQstdPooled
SA212748batch9_MT_20210803_001ECommercialQstdPooled
SA212749batch9_MT_20210803_089CommercialQstdPooled
SA212750batch9_MT_20210803_183CommercialQstdPooled
SA212751batch9_MT_20210803_185CommercialQstdPooled
SA212752batch9_MT_20210803_003KCommercialQstdPooled
SA212753batch9_MT_20210803_001ICommercialQstdPooled
SA212754batch9_MT_20210803_087CommercialQstdPooled
SA212755batch9_MT_20210803_003CCommercialQstdPooled
SA212756batch8_MT_20210802_001ICommercialQstdPooled
SA212757batch8_MT_20210802_191CommercialQstdPooled
SA212758batch8_MT_20210802_003KCommercialQstdPooled
SA212759batch9_MT_20210803_001CommercialQstdPooled
SA212760batch9_MT_20210803_001ACommercialQstdPooled
SA212761batch9_MT_20210803_003CommercialQstdPooled
SA212762batch7_MT_20210801_003CCommercialQstdPooled
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 268

Collection:

Collection ID:CO002312
Collection Summary:Two different deidentified human plasma pooled samples were used for this study: a) commercial Qstd plasma pool ; b) biosamples (from 1R01AI149746 (NIH-NIAID) samples) plasma pool
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002331
Treatment Summary:No treatment

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℃

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

MS:

MS ID:MS003394
Analysis ID:AN003643
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:None
Ion Mode:POSITIVE
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