Summary of Study ST001715

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 PR001099. The data can be accessed directly via it's Project DOI: 10.21228/M8N97J 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001715
Study TitleLarge-scale enzyme-based xenobiotic identification for exposomics
Study TypeXenobiotic Metabolism
Study SummaryExposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time, and co-occurrence with related xenobiotic metabolites. The data shared here are high-resolution Orbitrap MS data for S9 incubations of 140 xenobiotic compounds with 0 and 24 hour time points for all reactions.
Institute
Emory University
DepartmentMedicine
LaboratoryClinical Biomarkers Laboratory (Dean Jones, Ph.D PI)
Last NameLiu
First NameKen
Address615 Michael Street, Suite 225
Emailhkliu@emory.edu
Phone4047275984
Submit Date2021-02-21
Study CommentsNIEHS_U2C_140XenobioticReactions
Publicationshttps://assets.researchsquare.com/files/rs-77801/v1/7113b554-60b2-4a82-a93f-42e007637a00.pdf preprint
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2021-06-01
Release Version1
Ken Liu Ken Liu
https://dx.doi.org/10.21228/M8N97J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001099
Project DOI:doi: 10.21228/M8N97J
Project Title:Large-scale enzyme-based xenobiotic identification for exposomics
Project Type:Xenobiotic Metabolism
Project Summary:Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time, and co-occurrence with related xenobiotic metabolites. The data shared here are high-resolution Orbitrap MS data for S9 incubations of 140 xenobiotic compounds with 0 and 24 hour time points for all reactions.
Institute:Emory University
Department:Medicine
Laboratory:Clinical Biomarkers Laboratory (Dean Jones, Ph.D PI)
Last Name:Liu
First Name:Ken
Address:615 Michael Street, Suite 225, Atlanta, GA, 30329, USA
Email:hkliu@emory.edu
Phone:4047275091
Funding Source:U2CES026560

Subject:

Subject ID:SU001792
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Genotype Strain:Pooled Liver S9 fractions

Factors:

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

mb_sample_id local_sample_id Precursor
SA16043012_diphenylhydrazine_0_1_c18neg_fusion.mzXML12diphenylhydrazine | Time:-
SA16043112_diphenylhydrazine_0_2_hilicpos_fusion.mzXML12diphenylhydrazine | Time:-
SA16043212_diphenylhydrazine_0_2_c18neg_fusion.mzXML12diphenylhydrazine | Time:-
SA16043312_diphenylhydrazine_0_1_hilicpos_fusion.mzXML12diphenylhydrazine | Time:-
SA16043412_diphenylhydrazine_24_2_hilicpos_fusion.mzXML12diphenylhydrazine | Time:24
SA16043512_diphenylhydrazine_24_1_c18neg_fusion.mzXML12diphenylhydrazine | Time:24
SA16043612_diphenylhydrazine_24_2_c18neg_fusion.mzXML12diphenylhydrazine | Time:24
SA16043712_diphenylhydrazine_24_1_hilicpos_fusion.mzXML12diphenylhydrazine | Time:24
SA160438246_trichlorophenol_0_2_hilicpos_fusion.mzXML246trichlorophenol | Time:-
SA160439246_trichlorophenol_0_1_c18neg_fusion.mzXML246trichlorophenol | Time:-
SA160440246_trichlorophenol_0_2_c18neg_fusion.mzXML246trichlorophenol | Time:-
SA160441246_trichlorophenol_0_1_hilicpos_fusion.mzXML246trichlorophenol | Time:-
SA160442246_trichlorophenol_24_2_hilicpos_fusion.mzXML246trichlorophenol | Time:24
SA160443246_trichlorophenol_24_2_c18neg_fusion.mzXML246trichlorophenol | Time:24
SA160444246_trichlorophenol_24_1_hilicpos_fusion.mzXML246trichlorophenol | Time:24
SA160445246_trichlorophenol_24_1_c18neg_fusion.mzXML246trichlorophenol | Time:24
SA16044624_dimethylphenol_0_2_hilicpos_fusion.mzXML24dimethylphenol | Time:-
SA16044724_dimethylphenol_0_1_c18neg_fusion.mzXML24dimethylphenol | Time:-
SA16044824_dimethylphenol_0_2_c18neg_fusion.mzXML24dimethylphenol | Time:-
SA16044924_dimethylphenol_0_1_hilicpos_fusion.mzXML24dimethylphenol | Time:-
SA16045024_dimethylphenol_24_2_hilicpos_fusion.mzXML24dimethylphenol | Time:24
SA16045124_dimethylphenol_24_2_c18neg_fusion.mzXML24dimethylphenol | Time:24
SA16045224_dimethylphenol_24_1_hilicpos_fusion.mzXML24dimethylphenol | Time:24
SA16045324_dimethylphenol_24_1_c18neg_fusion.mzXML24dimethylphenol | Time:24
SA16045424_dinitrophenol_0_2_hilicpos_fusion.mzXML24dinitrophenol | Time:-
SA16045524_dinitrophenol_0_2_c18neg_fusion.mzXML24dinitrophenol | Time:-
SA16045624_dinitrophenol_0_1_hilicpos_fusion.mzXML24dinitrophenol | Time:-
SA16045724_dinitrophenol_0_1_c18neg_fusion.mzXML24dinitrophenol | Time:-
SA16045824_dinitrophenol_24_2_hilicpos_fusion.mzXML24dinitrophenol | Time:24
SA16045924_dinitrophenol_24_2_c18neg_fusion.mzXML24dinitrophenol | Time:24
SA16046024_dinitrophenol_24_1_hilicpos_fusion.mzXML24dinitrophenol | Time:24
SA16046124_dinitrophenol_24_1_c18neg_fusion.mzXML24dinitrophenol | Time:24
SA16046224_dinitrotoluene_0_2_hilicpos_fusion.mzXML24dinitrotoluene | Time:-
SA16046324_dinitrotoluene_0_2_c18neg_fusion.mzXML24dinitrotoluene | Time:-
SA16046424_dinitrotoluene_0_1_hilicpos_fusion.mzXML24dinitrotoluene | Time:-
SA16046524_dinitrotoluene_0_1_c18neg_fusion.mzXML24dinitrotoluene | Time:-
SA16046624_dinitrotoluene_24_2_hilicpos_fusion.mzXML24dinitrotoluene | Time:24
SA16046724_dinitrotoluene_24_2_c18neg_fusion.mzXML24dinitrotoluene | Time:24
SA16046824_dinitrotoluene_24_1_c18neg_fusion.mzXML24dinitrotoluene | Time:24
SA16046924_dinitrotoluene_24_1_hilicpos_fusion.mzXML24dinitrotoluene | Time:24
SA1604702_ethyl_hexyldiphenylphosphate_0_2_hilicpos_fusion.mzXML2ethylhexyldiphenylphosphate | Time:-
SA1604712_ethyl_hexyldiphenylphosphate_0_1_c18neg_fusion.mzXML2ethylhexyldiphenylphosphate | Time:-
SA1604722_ethyl_hexyldiphenylphosphate_0_2_c18neg_fusion.mzXML2ethylhexyldiphenylphosphate | Time:-
SA1604732_ethyl_hexyldiphenylphosphate_0_1_hilicpos_fusion.mzXML2ethylhexyldiphenylphosphate | Time:-
SA1604742_ethyl_hexyldiphenylphosphate_24_2_hilicpos_fusion.mzXML2ethylhexyldiphenylphosphate | Time:24
SA1604752_ethyl_hexyldiphenylphosphate_24_1_hilicpos_fusion.mzXML2ethylhexyldiphenylphosphate | Time:24
SA1604762_ethyl_hexyldiphenylphosphate_24_2_c18neg_fusion.mzXML2ethylhexyldiphenylphosphate | Time:24
SA1604772_ethyl_hexyldiphenylphosphate_24_1_c18neg_fusion.mzXML2ethylhexyldiphenylphosphate | Time:24
SA1604782_methyl_46_dinitrophenol_0_1_hilicpos_fusion.mzXML2methyl46dinitrophenol | Time:-
SA1604792_methyl_46_dinitrophenol_0_1_c18neg_fusion.mzXML2methyl46dinitrophenol | Time:-
SA1604802_methyl_46_dinitrophenol_0_2_c18neg_fusion.mzXML2methyl46dinitrophenol | Time:-
SA1604812_methyl_46_dinitrophenol_0_2_hilicpos_fusion.mzXML2methyl46dinitrophenol | Time:-
SA1604822_methyl_46_dinitrophenol_24_2_hilicpos_fusion.mzXML2methyl46dinitrophenol | Time:24
SA1604832_methyl_46_dinitrophenol_24_1_hilicpos_fusion.mzXML2methyl46dinitrophenol | Time:24
SA1604842_methyl_46_dinitrophenol_24_1_c18neg_fusion.mzXML2methyl46dinitrophenol | Time:24
SA1604852_methyl_46_dinitrophenol_24_2_c18neg_fusion.mzXML2methyl46dinitrophenol | Time:24
SA1604862_methylnaphthalene_0_2_hilicpos_fusion.mzXML2methylnapthalene | Time:-
SA1604872_methylnaphthalene_0_2_c18neg_fusion.mzXML2methylnapthalene | Time:-
SA1604882_methylnaphthalene_0_1_hilicpos_fusion.mzXML2methylnapthalene | Time:-
SA1604892_methylnaphthalene_0_1_c18neg_fusion.mzXML2methylnapthalene | Time:-
SA1604902_methylnaphthalene_24_1_c18neg_fusion.mzXML2methylnapthalene | Time:24
SA1604912_methylnaphthalene_24_1_hilicpos_fusion.mzXML2methylnapthalene | Time:24
SA1604922_methylnaphthalene_24_2_c18neg_fusion.mzXML2methylnapthalene | Time:24
SA1604932_methylnaphthalene_24_2_hilicpos_fusion.mzXML2methylnapthalene | Time:24
SA1604942_methylphenol_0_2_hilicpos_fusion.mzXML2methylphenol | Time:-
SA1604952_methylphenol_0_1_hilicpos_fusion.mzXML2methylphenol | Time:-
SA1604962_methylphenol_0_1_c18neg_fusion.mzXML2methylphenol | Time:-
SA1604972_methylphenol_0_2_c18neg_fusion.mzXML2methylphenol | Time:-
SA1604982_methylphenol_24_1_hilicpos_fusion.mzXML2methylphenol | Time:24
SA1604992_methylphenol_24_1_c18neg_fusion.mzXML2methylphenol | Time:24
SA1605002_methylphenol_24_2_hilicpos_fusion.mzXML2methylphenol | Time:24
SA1605012_methylphenol_24_2_c18neg_fusion.mzXML2methylphenol | Time:24
SA16050233_dichlorobenzidine_0_2_c18neg_fusion.mzXML33dichlorobenzidine | Time:-
SA16050333_dichlorobenzidine_0_2_hilicpos_fusion.mzXML33dichlorobenzidine | Time:-
SA16050433_dichlorobenzidine_0_1_hilicpos_fusion.mzXML33dichlorobenzidine | Time:-
SA16050533_dichlorobenzidine_0_1_c18neg_fusion.mzXML33dichlorobenzidine | Time:-
SA16050633_dichlorobenzidine_24_2_hilicpos_fusion.mzXML33dichlorobenzidine | Time:24
SA16050733_dichlorobenzidine_24_2_c18neg_fusion.mzXML33dichlorobenzidine | Time:24
SA16050833_dichlorobenzidine_24_1_c18neg_fusion.mzXML33dichlorobenzidine | Time:24
SA16050933_dichlorobenzidine_24_1_hilicpos_fusion.mzXML33dichlorobenzidine | Time:24
SA16051044_methylenebis(2_chloroaniline)_0_2_c18neg_fusion.mzXML44methylenebis2chloroaniline | Time:-
SA16051144_methylenebis(2_chloroaniline)_0_2_hilicpos_fusion.mzXML44methylenebis2chloroaniline | Time:-
SA16051244_methylenebis(2_chloroaniline)_0_1_c18neg_fusion.mzXML44methylenebis2chloroaniline | Time:-
SA16051344_methylenebis(2_chloroaniline)_0_1_hilicpos_fusion.mzXML44methylenebis2chloroaniline | Time:-
SA16051444_methylenebis(2_chloroaniline)_24_2_hilicpos_fusion.mzXML44methylenebis2chloroaniline | Time:24
SA16051544_methylenebis(2_chloroaniline)_24_2_c18neg_fusion.mzXML44methylenebis2chloroaniline | Time:24
SA16051644_methylenebis(2_chloroaniline)_24_1_c18neg_fusion.mzXML44methylenebis2chloroaniline | Time:24
SA16051744_methylenebis(2_chloroaniline)_24_1_hilicpos_fusion.mzXML44methylenebis2chloroaniline | Time:24
SA1605184_Ethylaniline_0_2_hilicpos_fusion.mzXML4ethylaniline | Time:-
SA1605194_Ethylaniline_0_2_c18neg_fusion.mzXML4ethylaniline | Time:-
SA1605204_Ethylaniline_0_1_hilicpos_fusion.mzXML4ethylaniline | Time:-
SA1605214_Ethylaniline_0_1_c18neg_fusion.mzXML4ethylaniline | Time:-
SA1605224_Ethylaniline_24_2_hilicpos_fusion.mzXML4ethylaniline | Time:24
SA1605234_Ethylaniline_24_2_c18neg_fusion.mzXML4ethylaniline | Time:24
SA1605244_Ethylaniline_24_1_c18neg_fusion.mzXML4ethylaniline | Time:24
SA1605254_Ethylaniline_24_1_hilicpos_fusion.mzXML4ethylaniline | Time:24
SA1605264_methylphenol_0_2_hilicpos_fusion.mzXML4methylphenol | Time:-
SA1605274_methylphenol_0_1_c18neg_fusion.mzXML4methylphenol | Time:-
SA1605284_methylphenol_0_2_c18neg_fusion.mzXML4methylphenol | Time:-
SA1605294_methylphenol_0_1_hilicpos_fusion.mzXML4methylphenol | Time:-
Showing page 1 of 13     Results:    1  2  3  4  5  Next  Last     Showing results 1 to 100 of 1232

Collection:

Collection ID:CO001785
Collection Summary:At the specified time point, S9 Reactions were extracted with 2x volume acetonitrile, and spun down at 14,000 rpm for 10 minutes and supernatants were transferred to autosampler vials. Samples were kept at -20°C until instrumental analysis.
Sample Type:Liver
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001805
Treatment Summary:Xenobiotic precursors were incubated with pooled human liver S9 fractions with an NADPH regenerating system and other required cofactors and collected at specified time points as described in the associated manuscript.

Sample Preparation:

Sampleprep ID:SP001798
Sampleprep Summary:Each test compound stock solution was diluted to 0.3 mM with water prior to incubation with S9 enzymes. The NADPH regenerating system was reconstituted with addition of 3.5 ml of water to make a nal volume of 5 ml. Cofactors were combined to form a 4X cofactor stock as follows, prior to addition into the reaction mixture: 10 mM UDPGA, 2 mM GSH, 2 mg/ml PAPS, 0.1 mM acetyl-CoA, and NADPH regenerating system (1 mM NADP, 5 mM glucose-6-phosphate, 1 unit glucose-6-phosphate dehydrogenase). Reactions were carried out at 30 °C on 96-well plates (Fig. 1). S9 fraction was diluted 10-fold in water immediately before mixing with 0.2 M Tris-Cl, pH 7.5/2 mM MgCl2 and 0.3 mM of the xenobiotic solution in a 1:1:1 ratio (15 µL each). and incubated at 30 °C for 5 min. To start the reaction, 15 µL of 4X cofactor stock was added, and incubation was carried out at 30 °C for the indicated times. To terminate the reaction, we added a three-fold volume of acetonitrile, covered the plate with paralm, vortexed, and froze at − 20 °C to precipitate insoluble materials such as protein. After thawing and centrifugation of the incubation plate, the supernatants were transferred into polypropylene autosampler vials, which were stored at − 20 °C until instrumental analysis

Combined analysis:

Analysis ID AN002792 AN002793 AN002794 AN002795
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters XBridge BEH Amide (50mm x 2.1mm,2.5um) Waters XBridge BEH Amide (50mm x 2.1mm,2.5um) Higgins Analytical Targa C18 (50 x 2.1mm,3um) Higgins Analytical Targa C18 (50 x 2.1mm,3um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Fusion Tribrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Fusion Tribrid Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units relative intensity relative intensity relative intensity relative intensity

Chromatography:

Chromatography ID:CH002065
Chromatography Summary:HILIC/ESI+
Chromatography Comments:HFQE
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge BEH Amide (50mm x 2.1mm,2.5um)
Chromatography Type:HILIC
  
Chromatography ID:CH002066
Chromatography Summary:C18/ESI-
Chromatography Comments:HFQE
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Higgins Analytical Targa C18 (50 x 2.1mm,3um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002588
Analysis ID:AN002792
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:PRM MSMS, ddMSMS and MS1 data collection, mzmine2
Ion Mode:POSITIVE
  
MS ID:MS002589
Analysis ID:AN002793
Instrument Name:Thermo Fusion Tribrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:ddMSMS and MS1 data collection. mzmine2
Ion Mode:POSITIVE
  
MS ID:MS002590
Analysis ID:AN002794
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:PRM MSMS, ddMSMS and MS1 data collection. mzmine2
Ion Mode:NEGATIVE
  
MS ID:MS002591
Analysis ID:AN002795
Instrument Name:Thermo Fusion Tribrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:ddMSMS and MS1 data collection. mzmine2
Ion Mode:NEGATIVE
  logo