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"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002233","ANALYSIS_ID":"AN003643","VERSION":"1","CREATED_ON":"July 24, 2022, 7:29 am"},

"PROJECT":{"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)"},

"STUDY":{"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","EMAIL":"amnah.siddiqa@jax.org","PHONE":"404-918 7223"},

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{
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},
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},
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{
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},
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},
{
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"Sample ID":"batch9_MT_20210803_183",
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},
{
"Subject ID":"-",
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{
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{
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],
"COLLECTION":{"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_SUMMARY":"No treatment"},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Scientific Vanquish Horizon UHPLC system","COLUMN_NAME":"HILIC column, AccucoreTM-150-Amide 50 x 2.1 x 2.6 μ","COLUMN_TEMPERATURE":"45°C"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap ID-X tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"None","MS_RESULTS_FILE":"ST002233_AN003643_Results.txt UNITS:m/z values Has m/z:Yes Has RT:Yes RT units:Seconds"}

}