{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003075","ANALYSIS_ID":"AN005033","VERSION":"1","CREATED_ON":"03-02-2024"},

"PROJECT":{"PROJECT_TITLE":"Evaluation of a python-centric metabolomics data processing pipeline based on Asari.","PROJECT_SUMMARY":"To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics. The uploaded datasets include previously unreleased datasets used for the evaluation of this pipeline including two large plasma datasets taken from recipients of one of two herpes zoster vaccines, analyzed as 17 separate batches, and a lipidomics dataset collected on a subset of these patients.","INSTITUTE":"Jackson Laboratory for Genomic Medicine","LABORATORY":"Shuzhao Li Laboratory","LAST_NAME":"Joshua","FIRST_NAME":"Mitchell","ADDRESS":"10 Discovery Dr, Farmington CT 06032","EMAIL":"joshua.mitchell@jax.org","PHONE":"8608372474","FUNDING_SOURCE":"NIH grants U01 CA235493 (NCI), R01 AI149746 and AI149746 S1 (NIAID), and UM1 HG012651 (NHGRI).","PUBLICATIONS":"Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline (BioRxiv) Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li; doi: https://doi.org/10.1101/2024.02.13.580048","DOI":"http://dx.doi.org/10.21228/M86137","CONTRIBUTORS":"Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Shuzhao Li"},

"STUDY":{"STUDY_TITLE":"HZV029 TwoPhase Metabolomics and Lipidomics","STUDY_SUMMARY":"In this study, a subset of plasma samples were processed using an in-house two phase extraction protocol based on the protocol originally proposed by Matayash et al. The resulting non-polar layer was then analyzed on a Thermo ScientificTM TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization source. This dataset was collected as a single batch and was used for the pipeline's ability to detect failed injections, which in this study, was simulated through the substitution of an empty vial for a missing study sample.","INSTITUTE":"Jackson Laboratory for Genomic Medicine","LABORATORY":"Shuzhao Li Laboratory","LAST_NAME":"Joshua","FIRST_NAME":"Mitchell","ADDRESS":"10 Discovery Dr, Farmington CT 06032","EMAIL":"joshua.mitchell@jax.org","PHONE":"8608372474","SUBMIT_DATE":"2024-02-15"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
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"Sample ID":"pooledsample_DDA_01",
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{
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"Sample ID":"pooledsample_DDA_02",
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{
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"Subject ID":"-",
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{
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{
"Subject ID":"-",
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{
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},
{
"Subject ID":"-",
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{
"Subject ID":"-",
"Sample ID":"MT_20230807_072",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
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},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_073",
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},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_074",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_074.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_077",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
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},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_078",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
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{
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{
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{
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},
{
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"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
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},
{
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"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
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},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_084",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_084.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_085",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_085.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_086",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_086.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_087",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_087.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_088",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_088.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_089",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_089.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_090",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_090.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_091",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_091.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_092",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_092.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_093",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_093.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_094",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_094.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_095",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_095.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_096",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_096.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_099",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_099.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_100",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_100.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_101",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_101.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_102",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_102.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_103",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_103.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_104",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_104.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_105",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_105.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_106",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_106.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_107",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_107.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_108",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_108.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_109",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_109.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_110",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_110.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_111",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_111.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_112",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_112.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_113",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_113.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_114",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_114.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_115",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_115.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_116",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_116.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_117",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_117.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_118",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_118.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_119",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_119.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_120",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_120.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_121",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_121.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"MT_20230807_122",
"Factors":{"Factor":"Unknown","Sample source":"Plasma"},
"Additional sample data":{"RAW_FILE_NAME":"MT_20230807_122.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Deidentified human plasma samples were used for this study: a) commercial Qstd and NIST plasma pool ; b) biosamples (from 1R01AI149746 (NIH-NIAID) samples) plasma, collected through venipuncture.","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Not applicable."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma samples were extracted following an in-house two-phase extraction protocol using methyl tert-butyl ether (MTBE) and methanol as a non-polar and polar extraction solvent and water as a phase separation solvent. The polar phase was used for metabolomics and non-polar phase for lipidomics studies. The MTBE method was introduced by Matayash 2008 which is modified and optimized. Briefly, 100 ml of ice-cold methanol and 300 ml of ice-cold MTBE was added each PBMC pellet to extract polar and non-polar lipid molecules, respectively. For a phase separation, 100 ml of ice-cold water was used. 4 μl of IS solution prepared by mixing 0.12 mL of 1 M D-Glucose-13C6, 0.2 mL of 5 mM Caffeine-3-methyl-13C, 0.6 mL of 10 mM L-Methionine-13C5, 0.6 mL of 20 mM L-Glutamic acid-13C5, 0.8 mL of 10 mM Uracil-15N2, 4 mL of 2 mM L-Tyrosine-15N and 3.68 mL water in 15-mL tube was added in each sample as spike-in controls for polar phase extraction. 10 ml of stable isotope labeled standards (Avanti SPLASH Lipidomix), representing differing lipid classes, were added to each sample to use as a spike ins quality control for non-polar phase extraction. All samples were vortexed (Vortex-Genie 2, Scientific Industries, cat. no. SI-0236) and incubated with shaking ((Eppendorf Thermo Mixer C) at 1000 rpm for 20 min at 4 °C followed by centrifugation at 4 °C for 15 min at 20,817 × g (Centrifuge 5430 R, Eppendorf). 100 ml of lower polar phase for metabolomics were transferred to 1.5 mL autosampler vial and 3 ml injected directly into UHPLC-MS. 250 ml of upper non-polar MTBE phase was transferred to new tube and dried for 2 hrs at Labconco CentriVap Centrifugal Vacuum Concentrator (CentriVap Benchtop Centrifugal Vacuum Concentrator with acrylic lid, Labconco Corporation, cat. no. 7810010), followed by resuspending in 70 ml of methanol:toulene (8:1, v/v) solution. 3 ml of reconstituted solution was injected into UHPLC-MS. For quality control (QC) and assurance (QA), 10 ml of methanol extract from each sample of batch 1 was collected and pooled together to prepare QC sample for polar phase metabolomics. Similarly, 10 ml of reconstituted methanol:toluene (8:1, v/v) solution from each sample of batch 1 was collected and pooled together to prepare QC sample to be used for non-polar phase lipidomics."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The chromatographic separations were performed using Thermo ScientificTM TranscendTM Duo LX-2 UHPLC system interfaced with high resolution Thermo ScientificTM Orbitrap ID-XTM TribidTM mass spectrometer with a HESI ionization source, using both positive and negative ionization mode with a run time of 8.5 min for polar and 12 min for non-polar extract. All samples were maintained at 4 °C in the autosampler. Data were acquired for polar and non-polar extract using HILIC, respectively in full scan mode with mass resolution of 60,000. An AccucoreTM-150-Amide HILIC column (2.6 mm, 2.1 mm x 100 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) was used for polar extract. 10 mM ammonium acetate in acetonitrile:water (95:5, v/v) with 0.1% acetic acid as mobile phase A and 10 mM ammonium acetate in acetonitrile:water (50:50, v/v) with 0.1% acetic acid as mobile phase B were used for HILIC method. For HILIC acquisition, following gradient was applied at a flow rate of 0.55 ml/min: 0-0.2 min: 0% B, 0.20-8.75 min: 98% B, and 11.25 min for cleaning and equilibration of column. Mass spectrometry data were collected with the following MS settings: mass range, 100-1700 m/z for lipidomics and 60-1000 for metabolomics; spray voltage, 3200 V (ESI+), 2800 V (ESI-); sheath gas, 45 Arb; auxiliary gas, 20 Arb; sweep gas, 1 Arb; ion transfer tube temperature, 325 °C; vaporizer temperature, 325 °C; full scan mass resolution, 60,000 (MS1); normalized AGC target (%), 25; maximum injection time, 100 ms. Data dependent fragmentation (dd-MS/MS) parameters for each polarity as follows: isolation window (m/z), 1.2; stepped HCD collision energy (%), 20,40,80; dd-MS/MS resolution, 30,000; normalized AGC target (%), 20; maximum injection time (ms), 54; micro scan, 1; cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to collect MS2 spectra for identification of compounds.","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Accucore HILIC (100 x 2.1mm,2.6um)","COLUMN_TEMPERATURE":"45","FLOW_GRADIENT":"0-0.2 min: 0% B, 0.20-8.75 min: 98% B, and 11.25 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"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap ID-X tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Mass spectrometry data were collected with the following MS settings: mass range, 100-1700 m/z for lipidomics and 60-1000 for metabolomics; spray voltage, 3200 V (ESI+), 2800 V (ESI-); sheath gas, 45 Arb; auxiliary gas, 20 Arb; sweep gas, 1 Arb; ion transfer tube temperature, 325 °C; vaporizer temperature, 325 °C; full scan mass resolution, 60,000 (MS1); normalized AGC target (%), 25; maximum injection time, 100 ms. Data dependent fragmentation (dd-MS/MS) parameters for each polarity as follows: isolation window (m/z), 1.2; stepped HCD collision energy (%), 20,40,80; dd-MS/MS resolution, 30,000; normalized AGC target (%), 20; maximum injection time (ms), 54; micro scan, 1; cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to collect MS2 spectra.","ION_MODE":"NEGATIVE","MS_RESULTS_FILE":"ST003075_AN005033_Results.txt UNITS:peak intensity Has m/z:Yes Has RT:Yes RT units:Seconds"}

}