Summary of Study ST004030

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 PR002522. The data can be accessed directly via it's Project DOI: 10.21228/M8NG10 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.

Study ID	ST004030
Study Title	StAR-MS for indole derivative discovery in mice feces
Study Summary	We present structure-to-activity-relationship metabolomics (StAR-MS), a framework aiming at elucidating the inherent SAR information embedded within non-targeted metabolomics data guided by fragment (substructure)-activity knowledge.CV C57BL/6J male mice (n=15) and GF C57BL/6J male mice derived from the UNC National Gnotobiotic Rodent Resource Center (n=9) were housed separately, with urine and feces samples collected. The fecal samples were pre-treated to extract metabolites for untargeted metabolomics analysis. A total of 22 metabolites exhibiting activity-related substructures were identified, four of which were characterized for the first time.
Institute	University of North Carolina at Chapel Hill
Department	ESE
Laboratory	Lu lab
Last Name	Zhao
First Name	Haoduo
Address	135 Dauer Drive Chapel Hill, NC 27599-7400
Email	raven456@unc.edu
Phone	19845281428
Submit Date	2025-07-01
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-07-30
Release Version	1

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Project:

Project ID:	PR002522
Project DOI:	doi: 10.21228/M8NG10
Project Title:	StAR-MS for indole derivative discovery in mice feces
Project Summary:	Human intestinal microbiota exert significant influences on host physiology through bioactive molecules. Indole derivatives, a diverse class of organic compounds arising from microbial-mediated tryptophan metabolism, play pivotal roles in maintaining metabolic homeostasis and disease progression. The characteristic aromatic heterocycle substructure shared in various indole derivatives is intrinsically associated with the activation of aryl hydrocarbon receptor (AhR), suggesting a potential structure-activity relationship (SAR) which remains underexplored. In the present study, we developed a structure-to-activity relationship metabolomics (StAR-MS) pipeline that aims at elucidating the SAR information embedded within metabolomics data, further applied it to identify novel gut microbiome-derived, indole-like derivatives with potential AhR agonistic activity. A total of 22 metabolites exhibiting activity-related substructures were identified, four of which were characterized for the first time.
Institute:	University of North Carolina at Chapel Hill
Department:	ESE
Laboratory:	Lu lab
Last Name:	Zhao
First Name:	Haoduo
Address:	135 Dauer Drive Chapel Hill, NC 27599-7400
Email:	raven456@unc.edu
Phone:	9845281428

Subject:

Subject ID:	SU004176
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

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

mb_sample_id	local_sample_id	Sample source	Mass spec config
SA464693	Mice372-WT-Feces	Conventional Raised	Full MS1
SA464694	Mice379-WT-Feces	Conventional Raised	Full MS1
SA464695	Mice377-WT-Feces	Conventional Raised	Full MS1
SA464696	Mice376-WT-Feces	Conventional Raised	Full MS1
SA464697	Mice374-WT-Feces	Conventional Raised	Full MS1
SA464698	Mice373-WT-Feces	Conventional Raised	Full MS1
SA464699	Mice369-WT-Feces	Conventional Raised	Full MS1
SA464700	Mice371-WT-Feces	Conventional Raised	Full MS1
SA464701	Mice381-WT-Feces	Conventional Raised	Full MS1
SA464702	Mice370-WT-Feces	Conventional Raised	Full MS1
SA464703	Mice380-WT-Feces	Conventional Raised	Full MS1
SA464704	Mice378-WT-Feces	Conventional Raised	Full MS1
SA464705	Mice382-WT-Feces	Conventional Raised	Full MS1
SA464706	Mice383-WT-Feces	Conventional Raised	Full MS1
SA464707	Mice384-WT-Feces	Conventional Raised	Full MS1
SA464708	CR-103	Conventional Raised	Precursor scan
SA464709	CR-130	Conventional Raised	Precursor scan
SA464710	CR-89+116	Conventional Raised	Precursor scan
SA464711	Mice360-GF-Feces	Germ free	Full MS1
SA464712	Mice361-GF-Feces	Germ free	Full MS1
SA464713	Mice362-GF-Feces	Germ free	Full MS1
SA464714	Mice364-GF-Feces	Germ free	Full MS1
SA464715	Mice365-GF-Feces	Germ free	Full MS1
SA464716	Mice366-GF-Feces	Germ free	Full MS1
SA464717	Mice367-GF-Feces	Germ free	Full MS1
SA464718	Mice368-GF-Feces	Germ free	Full MS1
SA464719	Mice363-GF-Feces	Germ free	Full MS1

Showing results 1 to 27 of 27

Showing results 1 to 27 of 27

Collection:

Collection ID:	CO004169
Collection Summary:	This collection contains the Full MS1 and precursor ion scan result from GF/CR mice feces. Mice feces samples were harvested and conserved at −80°C until use (at least 150 mg each).
Sample Type:	Feces

Treatment:

Treatment ID:	TR004185
Treatment Summary:	CV C57BL/6J male mice (n=15) and GF C57BL/6J male mice derived from the UNC National Gnotobiotic Rodent Resource Center (n=9) were housed separately, with urine and feces samples collected.

Sample Preparation:

Sampleprep ID:	SP004182
Sampleprep Summary:	This protocol was designed for the extraction of fecal metabolite from mice feces sample 2. Fecal samples were first thawed on ice and weighed. 100 µL water and 30 mg feces were mixed in Eppendorf tube, with ~ 30 mg glass beads added. Then, fecal samples were homogenized with TissueLyzer (50 Hz, 10 min). 400 µL methanol were added for a 30 mg sample and incubated at -20°C for 1 hour to ensure deproteinization. The samples were centrifuged 15,000 x g for 10 min, followed by collecting 400 µL supernatant and dry with SpeedVac®. The dried samples were further reconstituted with 150 μL 2% acetonitrile in water and vortexed vigorously. Finally, the samples were centrifuged again at 15,000 x g for 10 min with supernatant collected in glass vial. Fecal metabolite samples were now ready for LC-MS analysis. This protocol was designed for the extraction of fecal metabolite from mice tissue sample. Tissue samples were first thawed on ice and weighed. 300 µL water and 30 mg feces were mixed in Eppendorf tube, with 1 stainless bead added. Then, tissue samples were homogenized with TissueLyzer (50 Hz, 10 min). Add 1,200 µL acetonitrile for 30 µg tissue and incubated at -20°C for 1 hr. The samples were centrifuged 15,000 x g at 4°C for 10 min, followed by collecting 1000 µL supernatant and dry with SpeedVac®. The dried samples were further reconstituted with 150 μL 2% acetonitrile in water and vortexed vigorously. Finally, the samples were centrifuged again at 15,000 x g for 10 min with supernatant collected in glass vial. Fecal metabolite samples were now ready for LC-MS analysis.

Sampleprep ID:

SP004182

Sampleprep Summary:

This protocol was designed for the extraction of fecal metabolite from mice feces sample 2. Fecal samples were first thawed on ice and weighed. 100 µL water and 30 mg feces were mixed in Eppendorf tube, with ~ 30 mg glass beads added. Then, fecal samples were homogenized with TissueLyzer (50 Hz, 10 min). 400 µL methanol were added for a 30 mg sample and incubated at -20°C for 1 hour to ensure deproteinization. The samples were centrifuged 15,000 x g for 10 min, followed by collecting 400 µL supernatant and dry with SpeedVac®. The dried samples were further reconstituted with 150 μL 2% acetonitrile in water and vortexed vigorously. Finally, the samples were centrifuged again at 15,000 x g for 10 min with supernatant collected in glass vial. Fecal metabolite samples were now ready for LC-MS analysis. This protocol was designed for the extraction of fecal metabolite from mice tissue sample. Tissue samples were first thawed on ice and weighed. 300 µL water and 30 mg feces were mixed in Eppendorf tube, with 1 stainless bead added. Then, tissue samples were homogenized with TissueLyzer (50 Hz, 10 min). Add 1,200 µL acetonitrile for 30 µg tissue and incubated at -20°C for 1 hr. The samples were centrifuged 15,000 x g at 4°C for 10 min, followed by collecting 1000 µL supernatant and dry with SpeedVac®. The dried samples were further reconstituted with 150 μL 2% acetonitrile in water and vortexed vigorously. Finally, the samples were centrifuged again at 15,000 x g for 10 min with supernatant collected in glass vial. Fecal metabolite samples were now ready for LC-MS analysis.

Chromatography:

Chromatography ID:	CH005062
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm)
Column Temperature:	40°C
Flow Gradient:	2%B, 0–1 min; 2 to 15% B, 1–3 min; 15 to 50% B, 3–6 min; 50 to 98% B, 6–7.5 min;98% B, 7.5–11.5 min; 98 to 2% B, 11.5–11.6 min; 2% B, 11.6–15 min.
Flow Rate:	0.4 mL/min
Solvent A:	0.1% formic acid in water
Solvent B:	0.1% formic acid in ACN
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN006661
Analysis Type:	MS
Chromatography ID:	CH005062
Num Factors:	3
Num Metabolites:	19
Units:	intensity