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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002174 |
| Study Title | Identifying a tryptophan derivative in hydrogen peroxide-treated cell culture medium |
| Study 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 |
| ByeongHyeok.Choi@nyulangone.org | |
| Phone | 2122635521 |
| Submit Date | 2022-04-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-06-01 |
| Release Version | 1 |
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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 |
|---|---|---|
| SA208954 | 19 +DON 13C 3 | +DON |
| SA208955 | 19 +DON 13C 2 | +DON |
| SA208956 | 19 +DON 13C 1 | +DON |
| SA208957 | 19 +DON 15N 1 | DON |
| SA208958 | 19 +DON 15N 2 | DON |
| SA208959 | 19 +DON 15N 3 | DON |
| SA208960 | 19 NT 15N 3 | NT |
| SA208961 | 19 NT 15N 1 | NT |
| SA208962 | 19 NT 15N 2 | NT |
| SA208963 | 19 NT 13C 2 | VEH |
| SA208964 | 19 NT 13C 1 | VEH |
| SA208965 | 19 NT 13C 3 | VEH |
| 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 (150 x 4.6mm,5um) |
| 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 (150 x 4.6mm,5um) |
| Column Pressure: | 1800 |
| Column Temperature: | 25 |
| Flow Rate: | 0.100ml/min |
| Injection Temperature: | 4 |
| Internal Standard: | ISTD (500nM amino acid cocktail) |
| Solvent A: | 100% water; 10 mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| 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 |
