Summary of study ST001176

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 PR000788. The data can be accessed directly via it's Project DOI: 10.21228/M8TM3P This work is supported by NIH grant, U2C- DK119886.

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Study IDST001176
Study TitleMetabolite changes in human plasma before and after YF17D vaccination in symptomatic and asymptomatic subjects
Study SummaryPlasma was taken before and 1 day post-YF17D vaccination in a total of 13 subjects, of which 6 were asymptomatic and 7 were symptomatic.
Institute
Duke-NUS Medical School
Last NameChan
First NameKuan Rong
Address8 College Road Singapore 169857, Singapore, Singapore, 169857, Singapore
Emailkuanrong.chan@duke-nus.edu.sg
Phone90058277
Submit Date2019-04-25
Num Groups2
Total Subjects13
Raw Data AvailableYes
Raw Data File Type(s).xlsx
Release Date2019-05-15
Release Version1
Kuan Rong Chan Kuan Rong Chan
https://dx.doi.org/10.21228/M8TM3P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000788
Project DOI:doi: 10.21228/M8TM3P
Project Title:Metabolite analysis of subjects before and after YF17D vaccination
Project Type:CE-MS/MS analysis
Project Summary:CE-MS/MS analysis of plasma from subjects given the Yellow Fever live-attenuated vaccine (YF17D). Plasma metabolites were measured before vaccination (day 0) or 1 day after vaccination.
Institute:Duke-NUS Medical School
Department:Emerging Infectious Diseases
Last Name:Chan
First Name:Kuan Rong
Address:8 College Road Singapore 169857, Singapore, Singapore, 169857, Singapore
Email:kuanrong.chan@duke-nus.edu.sg
Phone:90058277

Factors:

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

mb_sample_id local_sample_id Outcome Day post-vaccination
SA081573C1_d0Asymptomatic day 0
SA081574C6_d0Asymptomatic day 0
SA081575C5_d0Asymptomatic day 0
SA081576C2_d0Asymptomatic day 0
SA081577C3_d0Asymptomatic day 0
SA081578C4_d0Asymptomatic day 0
SA081579C6_d1Asymptomatic day 1
SA081580C5_d1Asymptomatic day 1
SA081581C2_d1Asymptomatic day 1
SA081582C1_d1Asymptomatic day 1
SA081583C4_d1Asymptomatic day 1
SA081584C3_d1Asymptomatic day 1
SA081585AE6_d0Symptomatic day 0
SA081586AE5_d0Symptomatic day 0
SA081587AE7_d0Symptomatic day 0
SA081588AE2_d0Symptomatic day 0
SA081589AE4_d0Symptomatic day 0
SA081590AE1_d0Symptomatic day 0
SA081591AE3_d0Symptomatic day 0
SA081592AE6_d1Symptomatic day 1
SA081593AE7_d1Symptomatic day 1
SA081594AE5_d1Symptomatic day 1
SA081595AE3_d1Symptomatic day 1
SA081596AE1_d1Symptomatic day 1
SA081597AE2_d1Symptomatic day 1
SA081598AE4_d1Symptomatic day 1

Treatment:

Treatment ID:TR001257
Treatment Summary:Subjects were all given the YF17D vaccine, of which 6 were asymptomatic and 7 were symptomatic after vaccination. Plasma was collected before (day 0) and 1 day post-YF17D vaccination

Collection:

Collection ID:CO001236
Collection Summary:Plasma collected from subjects in EDTA-treated tubes before (day 0) and 1 day post-YF17D vaccination
Sample Type:Blood (plasma)

Sample Preparation:

Sampleprep ID:SP001250
Sampleprep Summary:CE-MS/MS profiling was conducted by Basic Scan package of Human Metabolome Technologies (HMT) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS).Briefly, CE-TOFMS analysis was carried out using an Agilent CE capillary electrophoresis system equipped with an Agilent 6210 time-of-flight mass spectrometer, Agilent 1100 isocratic HPLC pump, Agilent G1603A CE-MS adapter kit, and Agilent G1607A CE-ESI-MS sprayer kit (Agilent Technologies, Waldbronn, Germany). The systems were controlled by Agilent G2201AA ChemStation software version B.03.01 for CE (Agilent Technologies) and connected by a fused silica capillary (50 μm i.d. × 80 cm total length) with commercial electrophoresis buffer (H3301-1001 and H3302-1021 for cation and anion analyses, respectively, HMT) as the electrolyte. The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using MasterHands, automatic integration software (Keio University, Tsuruoka, Yamagata, Japan) in order to obtain peak information including m/z, peak area, and migration time (MT)43. Signal peaks corresponding to isotopomers, adduct ions, and other product ions of known metabolites were excluded, and remaining peaks were annotated according to the HMT metabolite database based on their m/z values with the MTs. Areas of the annotated peaks were then normalized based on internal standard levels and sample volumes in order to obtain relative levels of each metabolite.

Combined analysis:

Analysis ID AN001952
Analysis type MS
Chromatography type Other
Chromatography system Agilent 6210
Column Agilent capillary electrophoresis system
MS Type Other
MS instrument type CE-TOFMS
MS instrument name Agilent 6210 TOF
Ion Mode UNSPECIFIED

Chromatography:

Chromatography ID:CH001415
Chromatography Summary:CEMS conducted by Basic Scan package of Human Metabolome 239 Technologies (HMT)
Instrument Name:Agilent 6210
Column Name:Agilent capillary electrophoresis system
Chromatography Type:Other

MS:

MS ID:MS001807
Analysis ID:AN001952
Instrument Name:Agilent 6210 TOF
Instrument Type:CE-TOFMS
MS Type:Other
MS Comments:The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using MasterHands, automatic integration software (Keio University, Tsuruoka, Yamagata, Japan) in order to obtain peak information including m/z, peak area, and migration time (MT)43. Signal peaks corresponding to isotopomers, adduct ions, and other product ions of known metabolites were excluded, and remaining peaks were annotated according to the HMT metabolite database based on their m/z values with the MTs. Areas of the annotated peaks were then normalized based on internal standard levels and sample volumes in order to obtain relative levels of each metabolite. Partial least square discriminant analysis was performed by HMT’s proprietary software, PeakStat and SampleStat, respectively. Pathway analysis is performed by MetaboAnalyst 4.0.
Ion Mode:UNSPECIFIED