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.

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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

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