Summary of Study ST002174

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 PR001383. The data can be accessed directly via it's Project DOI: 10.21228/M8Z993 This work is supported by NIH grant, U2C- DK119886.

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Study IDST002174
Study TitleIdentifying a tryptophan derivative in hydrogen peroxide-treated cell culture medium
Study SummaryReactive oxygen species (ROS) are by-products of metabolism of oxygen and they play an important role in normal homeostasis and cell signaling, as well as in the initiation of diseases including cancer when their production is upregulated. Thus, it is imperative to understand the cellular and molecular basis by which ROS impact on various biological and pathological processes. Here, we identified 2-oxindole, a tryptophan derivative, was a major catabolic product in hydrogen peroxide-treated cell culture medium. We used 2-oxindole to study its role in regulating AhR signaling and tryptophan metabolic pathways. We found that 2-oxindole significantly increased the activity of AhR, leading to enhanced expression of its downstream targets including cytochrome P450 genes.
Institute
NYU Langone Health
DepartmentDepartment of Biochemistry and Molecular Pharmacology
LaboratoryDai
Last NameChoi
First NameByeong Hyeok
Address341 East 25 Street New York, NY 10010
EmailByeongHyeok.Choi@nyulangone.org
Phone2122635521
Submit Date2022-04-06
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-06-01
Release Version1
Byeong Hyeok Choi Byeong Hyeok Choi
https://dx.doi.org/10.21228/M8Z993
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001383
Project DOI:doi: 10.21228/M8Z993
Project Title:Identifying a tryptophan derivative in hydrogen peroxide-treated cell culture medium
Project Summary:Reactive oxygen species (ROS) are by-products of metabolism of oxygen and they play an important role in normal homeostasis and cell signaling, as well as in the initiation of diseases including cancer when their production is upregulated. Thus, it is imperative to understand the cellular and molecular basis by which ROS impact on various biological and pathological processes. Here, we identified 2-oxindole, a tryptophan derivative, was a major catabolic product in hydrogen peroxide-treated cell culture medium. We used 2-oxindole to study its role in regulating AhR signaling and tryptophan metabolic pathways. We found that 2-oxindole significantly increased the activity of AhR, leading to enhanced expression of its downstream targets including cytochrome P450 genes.
Institute:NYU Langone Health
Department:Department of Biochemistry and Molecular Pharmacology
Laboratory:Dai
Last Name:Choi
First Name:Byeong Hyeok
Address:341 East 25 Street New York, NY 10010
Email:ByeongHyeok.Choi@nyulangone.org
Phone:212-263-5521
Funding Source:NCI/US Public Service Award
Contributors:Metabolomics Core Resource Laboratory

Subject:

Subject ID:SU002260
Subject Type:Other abiotic sample

Factors:

Subject type: Other abiotic sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA20895719 +DON 15N 1DON
SA20895819 +DON 15N 2DON
SA20895919 +DON 15N 3DON
SA20895419 +DON 13C 3+DON
SA20895519 +DON 13C 2+DON
SA20895619 +DON 13C 1+DON
SA20896019 NT 15N 3NT
SA20896119 NT 15N 1NT
SA20896219 NT 15N 2NT
SA20896319 NT 13C 2VEH
SA20896419 NT 13C 1VEH
SA20896519 NT 13C 3VEH
Showing results 1 to 12 of 12

Collection:

Collection ID:CO002253
Collection Summary:Treatment and sample collection summary Dulbecco’s Modified Eagle’s Medium (DMEM, Corning, NY) supplemented with 10% fetal bovine serum (Atlanta biologicals) were treated with or without 0.2 mM hydrogen peroxide for 30 min in room temperature in triplicate. After incubation samples were immediately frozen in -80C.
Sample Type:Media

Treatment:

Treatment ID:TR002272
Treatment Summary:Dulbecco’s Modified Eagle’s Medium (DMEM, Corning, NY) supplemented with 10% fetal bovine serum (Atlanta biologicals) were treated with or without 0.2 mM hydrogen peroxide for 30 min in room temperature in triplicate. After incubation samples were immediately frozen in -80C.

Sample Preparation:

Sampleprep ID:SP002266
Sampleprep Summary:Samples were extracted with methanol and in house cocktail of amino acids, acting as an internal standards. Samples were then homogenized and spun down, and supernatant was dried down. Dried down samples were reconstituted and transferred to LCMS vials, then injected on LCMS at 2ul per sample
Sampleprep Protocol ID:0.01.12.12
Processing Storage Conditions:4℃
Extraction Method:E.01
Extract Storage:-80℃
Sample Resuspension:50uL
Sample Spiking:500nM

Combined analysis:

Analysis ID AN003562
Analysis type MS
Chromatography type HILIC
Chromatography system Ulitmate 3000
Column SeQuant ZIC-pHILIC 5um polymer, 150x2.1mm
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units N/L

Chromatography:

Chromatography ID:CH002633
Chromatography Summary:SeQuant ZIC-pHILIC 5um polymer, 150x2.1mm - Part No. 15046000001 Buffer A: 10mM ammonium carbonate in water, LCMS Grade Buffer B: Acetonitrile, LCMS Grade Rear Wash: 10% methanol in water, LCMS Grade Wash Buffer: water, LCMS Grade Injection Volume: 2uL
Methods Filename:L12
Instrument Name:Ulitmate 3000
Column Name:SeQuant ZIC-pHILIC 5um polymer, 150x2.1mm
Column Pressure:1800
Column Temperature:25
Flow Rate:0.100ml/min
Injection Temperature:4
Internal Standard:ISTD (500nM amino acid cocktail)
Solvent A:Buffer A: 10mM ammonium carbonate in water, LCMS Grade
Solvent B:Buffer B: Acetonitrile, LCMS Grade
Chromatography Type:HILIC

MS:

MS ID:MS003319
Analysis ID:AN003562
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:M.13 Polar metabolites (pHILIC Hybrid).
Ion Mode:UNSPECIFIED
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