Summary of Study ST003075

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 PR001915. The data can be accessed directly via it's Project DOI: 10.21228/M86137 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 ID	ST003075
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
Publications	Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li doi: https://doi.org/10.1101/2024.02.13.580048
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2024-05-24
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001915
Project DOI:	doi: 10.21228/M86137
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
Contributors:	Joshua Mitchell, Yuanye Chi, Maheshwor Thapa, Shuzhao Li

Subject:

Subject ID:	SU003190
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	Factor	Sample source
SA332322	pooledsample_DDA_02	DDA	Pooled Study Plasma
SA332323	pooledsample_DDA_01	DDA	Pooled Study Plasma
SA332324	MT_20230807_007	NIST	Pooled NIST Reference Plasma
SA332325	MT_20230807_008	NIST	Pooled NIST Reference Plasma
SA332326	MT_20230807_124	Pooled	Pooled Study Plasma
SA332327	MT_20230807_010	Pooled	Pooled Study Plasma
SA332328	MT_20230807_123	Pooled	Pooled Study Plasma
SA332329	MT_20230807_032	Pooled	Pooled Study Plasma
SA332330	MT_20230807_076	Pooled	Pooled Study Plasma
SA332331	MT_20230807_075	Pooled	Pooled Study Plasma
SA332332	MT_20230807_054	Pooled	Pooled Study Plasma
SA332333	MT_20230807_053	Pooled	Pooled Study Plasma
SA332334	MT_20230807_098	Pooled	Pooled Study Plasma
SA332335	MT_20230807_097	Pooled	Pooled Study Plasma
SA332336	MT_20230807_009	Pooled	Pooled Study Plasma
SA332337	MT_20230807_031	Pooled	Pooled Study Plasma
SA332338	Blank_20230807_002	Process_Blank	Process Blank
SA332339	Blank_20230807_004	Process_Blank	Process Blank
SA332340	Blank_20230807_001	Process_Blank	Process Blank
SA332341	Blank_20230807_005	Process_Blank	Process Blank
SA332342	Blank_20230807_003	Process_Blank	Process Blank
SA332343	Blank_20230807_006	Process_Blank	Process Blank
SA332344	MT_20230807_005	QC	Pooled Commercial Plasma Sample
SA332345	MT_20230807_004	QC	Pooled Commercial Plasma Sample
SA332346	MT_20230807_006	QC	Pooled Commercial Plasma Sample
SA332347	MT_20230807_003	QC	Pooled Commercial Plasma Sample
SA332348	MT_20230807_001	QC	Pooled Commercial Plasma Sample
SA332349	MT_20230807_126	QC	Pooled Commercial Plasma Sample
SA332350	MT_20230807_002	QC	Pooled Commercial Plasma Sample
SA332351	MT_20230807_125	QC	Pooled Commercial Plasma Sample
SA332352	Sol_blank_20230807_004	Solvent_Blank	Solvent Blank
SA332353	Sol_blank_20230807_003	Solvent_Blank	Solvent Blank
SA332354	Sol_blank_20230807_002	Solvent_Blank	Solvent Blank
SA332355	Sol_blank_20230807_001	Solvent_Blank	Solvent Blank
SA332356	Blank_std_20230807_1_002	Standards_Blank	Blank w/ Stds
SA332357	Blank_std_20230807_1_001	Standards_Blank	Blank w/ Stds
SA332358	MT_20230807_091	Unknown	Plasma
SA332359	MT_20230807_090	Unknown	Plasma
SA332360	MT_20230807_089	Unknown	Plasma
SA332361	MT_20230807_095	Unknown	Plasma
SA332362	MT_20230807_093	Unknown	Plasma
SA332363	MT_20230807_094	Unknown	Plasma
SA332364	MT_20230807_092	Unknown	Plasma
SA332365	MT_20230807_082	Unknown	Plasma
SA332366	MT_20230807_080	Unknown	Plasma
SA332367	MT_20230807_081	Unknown	Plasma
SA332368	MT_20230807_079	Unknown	Plasma
SA332369	MT_20230807_078	Unknown	Plasma
SA332370	MT_20230807_077	Unknown	Plasma
SA332371	MT_20230807_096	Unknown	Plasma
SA332372	MT_20230807_083	Unknown	Plasma
SA332373	MT_20230807_087	Unknown	Plasma
SA332374	MT_20230807_086	Unknown	Plasma
SA332375	MT_20230807_085	Unknown	Plasma
SA332376	MT_20230807_084	Unknown	Plasma
SA332377	MT_20230807_088	Unknown	Plasma
SA332378	MT_20230807_104	Unknown	Plasma
SA332379	MT_20230807_115	Unknown	Plasma
SA332380	MT_20230807_116	Unknown	Plasma
SA332381	MT_20230807_114	Unknown	Plasma
SA332382	MT_20230807_113	Unknown	Plasma
SA332383	MT_20230807_112	Unknown	Plasma
SA332384	MT_20230807_117	Unknown	Plasma
SA332385	MT_20230807_118	Unknown	Plasma
SA332386	MT_20230807_122	Unknown	Plasma
SA332387	MT_20230807_121	Unknown	Plasma
SA332388	MT_20230807_120	Unknown	Plasma
SA332389	MT_20230807_119	Unknown	Plasma
SA332390	MT_20230807_074	Unknown	Plasma
SA332391	MT_20230807_111	Unknown	Plasma
SA332392	MT_20230807_103	Unknown	Plasma
SA332393	MT_20230807_102	Unknown	Plasma
SA332394	MT_20230807_101	Unknown	Plasma
SA332395	MT_20230807_100	Unknown	Plasma
SA332396	MT_20230807_105	Unknown	Plasma
SA332397	MT_20230807_106	Unknown	Plasma
SA332398	MT_20230807_110	Unknown	Plasma
SA332399	MT_20230807_109	Unknown	Plasma
SA332400	MT_20230807_108	Unknown	Plasma
SA332401	MT_20230807_107	Unknown	Plasma
SA332402	MT_20230807_099	Unknown	Plasma
SA332403	MT_20230807_061	Unknown	Plasma
SA332404	MT_20230807_030	Unknown	Plasma
SA332405	MT_20230807_033	Unknown	Plasma
SA332406	MT_20230807_029	Unknown	Plasma
SA332407	MT_20230807_028	Unknown	Plasma
SA332408	MT_20230807_026	Unknown	Plasma
SA332409	MT_20230807_027	Unknown	Plasma
SA332410	MT_20230807_034	Unknown	Plasma
SA332411	MT_20230807_035	Unknown	Plasma
SA332412	MT_20230807_039	Unknown	Plasma
SA332413	MT_20230807_040	Unknown	Plasma
SA332414	MT_20230807_038	Unknown	Plasma
SA332415	MT_20230807_037	Unknown	Plasma
SA332416	MT_20230807_036	Unknown	Plasma
SA332417	MT_20230807_025	Unknown	Plasma
SA332418	MT_20230807_024	Unknown	Plasma
SA332419	MT_20230807_015	Unknown	Plasma
SA332420	MT_20230807_016	Unknown	Plasma
SA332421	MT_20230807_014	Unknown	Plasma

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 140

Collection:

Collection ID:	CO003183
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 ID:	TR003199
Treatment Summary:	Not applicable.

Sample Preparation:

Sampleprep ID:	SP003196
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.

Sampleprep ID:

SP003196

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.

Combined analysis:

Analysis ID	AN005033
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Vanquish
Column	Thermo Accucore HILIC (100 x 2.1mm,2.6um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Orbitrap ID-X Tribrid
Ion Mode	NEGATIVE
Units	peak intensity

Chromatography:

Chromatography ID:	CH003804
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

MS:

MS ID:	MS004772
Analysis ID:	AN005033
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