Summary of Study ST002463

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 PR001590. The data can be accessed directly via it's Project DOI: 10.21228/M85Q7B 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 IDST002463
Study TitleTryptophan metabolites in mouse serum
Study SummaryAnalyzing murine sera to investigate into which tryptophan metabolites in the host circulation are derived from diet, host metabolism and/or the gut microbiome. Blood was collected from the portal vein of conventional C567BL/6J mice and sera analyzed by targeted LC-MS. To test this hypothesis and evaluate the necessity of microorganisms to produce these examined tryptophan metabolites, sera were collected from germ-free (GF) mice and subjected to the same targeted metabolomic analysis. Having generated Trp metabolite profiles from sera, we asked if altering the diet would significantly change circulating concentrations. One of two groups of conventional C57BL/6J mice with ad libitum access to a standard laboratory chow were switched onto a semi-purified diet (AIN-93G) while the second remained on standard chow. After one week, portal vein blood was collected and analyzed using targeted LC-MS.
Institute
Pennsylvania State University
Last NameDONG
First NameFANGCONG
Address309 Life Sciences Building, University Park, PA 16802
Emailfxd93@psu.edu
Phone8146990203
Submit Date2023-01-27
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-02-06
Release Version1
FANGCONG DONG FANGCONG DONG
https://dx.doi.org/10.21228/M85Q7B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001590
Project DOI:doi: 10.21228/M85Q7B
Project Title:Analyzing murine sera to investigate into which tryptophan metabolites in the host circulation are derived from diet, host metabolism and/or the gut microbiome.
Project Type:MS quantitative study
Project Summary:Analyzing murine sera to investigate into which tryptophan metabolites in the host circulation are derived from diet, host metabolism and/or the gut microbiome. Blood was collected from the portal vein of conventional C567BL/6J mice and sera analyzed by targeted LC-MS. To test this hypothesis and evaluate the necessity of microorganisms to produce these examined tryptophan metabolites, sera were collected from germ-free (GF) mice and subjected to the same targeted metabolomic analysis. Having generated Trp metabolite profiles from sera, we asked if altering the diet would significantly change circulating concentrations. One of two groups of conventional C57BL/6J mice with ad libitum access to a standard laboratory chow were switched onto a semi-purified diet (AIN-93G) while the second remained on standard chow. After one week, portal vein blood was collected and analyzed using targeted LC-MS.
Institute:The Pennsylvania State University
Last Name:DONG
First Name:FANGCONG
Address:309 Life Sciences Building, State college, PA, 16802, USA
Email:fxd93@psu.edu
Phone:8146990203

Subject:

Subject ID:SU002553
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id diluted factor
SA246429Batch2_std81
SA246430Batch2_std91
SA246431Batch2_std101
SA246432Batch2_std71
SA246433Batch2_std51
SA246434Batch2_std21
SA246435Batch2_std41
SA246436Batch3_std11
SA246437Batch2_std61
SA246438Batch3_std31
SA246439Batch3_std81
SA246440Batch3_std91
SA246441Batch3_std101
SA246442Batch3_std71
SA246443Batch3_std61
SA246444Batch2_std11
SA246445Batch3_std41
SA246446Batch3_std51
SA246447Batch3_std21
SA246448Batch2_std31
SA246449Batch1_std61
SA246450Batch1_std71
SA246451Batch1_std81
SA246452Batch1_std91
SA246453Batch1_std101
SA246454Batch1_std51
SA246455Batch1_std31
SA246456Batch1_std41
SA246457Batch1_std11
SA246458Batch1_std21
SA246459Batch3_SP61.25
SA246460Batch3_SP51.25
SA246461Batch3_SWT101.25
SA246462Batch3_SWT111.25
SA246463Batch3_SWT121.25
SA246464Batch3_SP41.25
SA246465Batch3_SWT91.25
SA246466Batch3_SWT81.25
SA246467Batch3_SWT71.25
SA246468Batch3_SP31.25
SA246469Batch3_SP21.25
SA246470Batch3_SP11.25
SA246471Batch2_SGF72.5
SA246472Batch2_Sconv12.5
SA246473Batch2_Sconv22.5
SA246474Batch1_SCH62.5
SA246475Batch1_SCH42.5
SA246476Batch1_SCH22.5
SA246477Batch1_SCH32.5
SA246478Batch2_Sconv32.5
SA246479Batch1_SCH52.5
SA246480Batch2_Sconv52.5
SA246481Batch2_SGF32.5
SA246482Batch2_SGF22.5
SA246483Batch2_SGF12.5
SA246484Batch1_SCH12.5
SA246485Batch2_SGF42.5
SA246486Batch2_SGF62.5
SA246487Batch2_SGF52.5
SA246488Batch2_Sconv42.5
Showing results 1 to 60 of 60

Collection:

Collection ID:CO002546
Collection Summary:Serum samples from conventional and GF mice were collected and stored at -80°C.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002565
Treatment Summary:Thawed on ice, 25 µL of serum sample, was mixed with 100 µL extraction solvent of ice-cold methanol containing indole-3-acetic acid-d4 and kynurenic acid-d5. Mixture was vortexed and incubated at −20 °C for 30 min. Following centrifugation at 12,000 × g for 15 min at 4℃, 90 µL supernatant was collected and subsequently evaporated to dryness (Thermo Scientific, Waltham, MA) and dissolved in 45 µL of 10% acetonitrile containing 1 µM chlorpropamide. After centrifugation at 12,000 × g for 15 min at 4℃, supernatants were transferred to autosampler vials for LC-MS analysis.

Sample Preparation:

Sampleprep ID:SP002559
Sampleprep Summary:GF mice were reared in standard, sterile (autoclaved cages containing sterile (autoclaved) bedding inside a hermetically sealed isolator with HEPA-filtered airflow and maintained on sterile (autoclaved) water and sterile (autoclaved) food (LabDiet® 5013, Land O’Lakes) ad libitum. One of two groups of conventional C57BL/6J mice with ad libitum access to a standard laboratory chow were switched onto a semi-purified diet (AIN-93G) while the second remained on standard chow. After one week, portal vein blood was collected.

Combined analysis:

Analysis ID AN004018
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple TOF
MS instrument name ABI Sciex 5600 TripleTOF
Ion Mode POSITIVE
Units uM

Chromatography:

Chromatography ID:CH002968
Instrument Name:Shimadzu 20AD
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:55
Flow Gradient:The initial condition were 97% A and 3 % B, increasing to 45% B at 10 min, 75% B at 12 min where it was held at 75% B until 17.5 min before returning to the initial conditions.
Flow Rate:0.25 mL/min
Solvent A:Water with 0.1% formic acid
Solvent B:Acetonitrile with 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003765
Analysis ID:AN004018
Instrument Name:ABI Sciex 5600 TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
MS Comments:Peakview was used for data analysis.
Ion Mode:POSITIVE
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