Summary of Study ST003109

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 IDST003109
Study TitleHZV029 Metabolomics
Study SummaryIn this study, plasma samples were processed using an in-house one phase extraction protocol as previously published (Siddiqa, A., et al., A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination. npj Vaccines, 2023. 8(1): p. 92. ). The resulting extract 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 over 17 batches and was used to evaluate the QA/QC metrics produced by the pipeline and resulting MS2 annotations generated from a complimentary AcquireX (deep scan) MS2 dataset were compared to compound discoverer.
Institute
Jackson Laboratory for Genomic Medicine
LaboratoryShuzhao Li Laboratory
Last NameJoshua
First NameMitchell
Address10 Discovery Dr, Farmington CT 06032
Emailjoshua.mitchell@jax.org
Phone8608372474
Submit Date2024-02-15
PublicationsCommon 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 AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-05-24
Release Version1
Mitchell Joshua Mitchell Joshua
https://dx.doi.org/10.21228/M86137
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU003224
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)

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Collection:

Collection ID:CO003217
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:TR003233
Treatment Summary:Not applicable.

Sample Preparation:

Sampleprep ID:SP003230
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.

Combined analysis:

Analysis ID AN005091 AN005092
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Accucore HILIC (100 x 2.1mm,2.6um) Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE
Units peak intensity peak intensity

Chromatography:

Chromatography ID:CH003847
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 positive and negative ionization modes. All samples were maintained at 4 °C in the autosampler. Data were acquired using hydrophilic interaction liquid chromatography (HILIC) and reversed phase (RP) column  in parallel both in positive and negative polarities in full scan mode with mass resolution of 120,000. An AccucoreTM−150-Amide HILIC column (2.6 μm, 2.1 mm × 50 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) and a Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) embedded with Hypersil GOLDTM RP guard column (2.1 mm x 10 mm, 3 μm) (Thermo Fisher Scientific, MA, USA. Cat. 25003-012101) maintained at 45 °C were used for chromatographic separation. 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. 0.1% formic acid in water and 0.1% formic acid in acetonitrile were used as mobile phase A and B respectively for RP acquisition. 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, and 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, and 5 min cleaning and column equilibration. This way the mass spec data for each sample was collected consecutively, carrying only one (either HILIC or RP) eluent to the MS for 5 min, while the other eluent was directed to the waste during washing and re-equilibration.
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore HILIC (100 x 2.1mm,2.6um)
Column Temperature:45
Flow Gradient:0–0.1 min: 0% B, 0.10–5.0 min: 98% B, and 5 min for cleaning and equilibration of column
Flow Rate:0.55 ml/min
Solvent A:95% acetonitrile/5% water; 10 mM ammonium acetate; 0.1% acetic acid
Solvent B:50% acetonitrile/50% water; 10 mM ammonium acetate; 0.1% acetic acid
Chromatography Type:HILIC
  
Chromatography ID:CH003848
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 positive and negative ionization modes. All samples were maintained at 4 °C in the autosampler. Data were acquired using hydrophilic interaction liquid chromatography (HILIC) and reversed phase (RP) column  in parallel both in positive and negative polarities in full scan mode with mass resolution of 120,000. An AccucoreTM−150-Amide HILIC column (2.6 μm, 2.1 mm × 50 mm) embedded with Accucore-150-Amide-HILIC guard column (10 × 2.1 mm, 2.6 μm) (Thermo Fisher Scientific, MA, USA. Cat. 16726-012105) and a Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm) embedded with Hypersil GOLDTM RP guard column (2.1 mm x 10 mm, 3 μm) (Thermo Fisher Scientific, MA, USA. Cat. 25003-012101) maintained at 45 °C were used for chromatographic separation. 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. 0.1% formic acid in water and 0.1% formic acid in acetonitrile were used as mobile phase A and B respectively for RP acquisition. 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, and 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, and 5 min cleaning and column equilibration. This way the mass spec data for each sample was collected consecutively, carrying only one (either HILIC or RP) eluent to the MS for 5 min, while the other eluent was directed to the waste during washing and re-equilibration.
Instrument Name:Thermo Vanquish
Column Name:Hypersil GOLDTM RP column (3 μm, 2.1 mm × 50 mm)
Column Temperature:45
Flow Gradient:0–0.1 min: 0% B, 0.10–1.9 min: 60% B, 1.9–5.0 min: 98% B, and 5 min cleaning and column equilibration
Flow Rate:0.4 ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004828
Analysis ID:AN005091
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, 80–1000 m/z; spray voltage, 3500 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, 120,000 (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; microscan, 1; cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to collect MS2 spectra for identification of compounds.
Ion Mode:POSITIVE
  
MS ID:MS004829
Analysis ID:AN005092
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, 80–1000 m/z; spray voltage, 3500 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, 120,000 (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; microscan, 1; cycle time (sec), 1.2. A full scan data-dependent MS2 (ddMS2) method was utilized to collect MS2 spectra for identification of compounds.
Ion Mode:NEGATIVE
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