Summary of Study ST003786

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 PR002363. The data can be accessed directly via it's Project DOI: 10.21228/M8653M 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	ST003786
Study Title	Molecular fingerprint inference reveals bioactive lipids and microbial metabolites in colitis
Study Type	Human Stool Ex vivo cultures
Study Summary	Untargeted metabolomics provides a sensitive readout of small molecules in biofluids, but requires targeted approaches to resolve ~90% of features for which tandem mass spectra (MS/MS) are not collected. By training on a subset of verified metabolites and their profiles in LC-MS, we derive a probabilistic model to predict molecular fingerprints in human stool and blood samples. These predictions, which do not utilize MS/MS, were accurate for >44% (correct top ranked candidate) or >75% (correct within top 3) of test metabolites, drastically reducing the number of reference standards that would need to be to be tested. These predictions revealed markers and drivers of inflammation, including amino acid derivatives and lysophospholipids with herein demonstrated platelet-activating factor receptor (PAF-R) activity. Integration with bacterial culturomics facilitates tracking the source of inflammation-associated metabolites to their origins in the gut microbiome.
Institute	Broad Institute of MIT and Harvard
Last Name	Avila-Pacheco
First Name	Julian
Address	415 Main Street
Email	jravilap@broadinstitute.org
Phone	(617) 714-1729
Submit Date	2025-03-04
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-08-04
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002363
Project DOI:	doi: 10.21228/M8653M
Project Title:	Molecular fingerprint inference reveals bioactive lipids and microbial metabolites in colitis
Project Summary:	Untargeted metabolomics provides a sensitive readout of small molecules in biofluids, but requires targeted approaches to resolve ~90% of features for which tandem mass spectra (MS/MS) are not collected. By training on a subset of verified metabolites and their profiles in LC-MS, we derive a probabilistic model to predict molecular fingerprints in human stool and blood samples. These predictions, which do not utilize MS/MS, were accurate for >44% (correct top ranked candidate) or >75% (correct within top 3) of test metabolites, drastically reducing the number of reference standards that would need to be to be tested. These predictions revealed markers and drivers of inflammation, including amino acid derivatives and lysophospholipids with herein demonstrated platelet-activating factor receptor (PAF-R) activity. Integration with bacterial culturomics facilitates tracking the source of inflammation-associated metabolites to their origins in the gut microbiome.
Institute:	Broad Institute of MIT and Harvard
Last Name:	Avila-Pacheco
First Name:	Julian
Address:	415 Main Street
Email:	jravilap@broadinstitute.org
Phone:	+1 (617) 714-1729

Subject:

Subject ID:	SU003920
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Sample source	Stool Donor	QCRole	Replicate	Time_point	Treatment
SA411120	288_1_0h	Human stool ex vivo culture	288	Sample	1	0h	-
SA411121	288m_1_0h	Human stool ex vivo culture	288	Sample	1	0h	Maslinic acid
SA411122	288_1_48h	Human stool ex vivo culture	288	Sample	1	48h	-
SA411123	288m_1_48h	Human stool ex vivo culture	288	Sample	1	48h	Maslinic acid
SA411124	288_2_0h	Human stool ex vivo culture	288	Sample	2	0h	-
SA411125	288m_2_0h	Human stool ex vivo culture	288	Sample	2	0h	Maslinic acid
SA411126	288_2_48h	Human stool ex vivo culture	288	Sample	2	48h	-
SA411127	288m_2_48h	Human stool ex vivo culture	288	Sample	2	48h	Maslinic acid
SA411128	288_3_0h	Human stool ex vivo culture	288	Sample	3	0h	-
SA411129	288m_3_0h	Human stool ex vivo culture	288	Sample	3	0h	Maslinic acid
SA411130	288_3_48h	Human stool ex vivo culture	288	Sample	3	48h	-
SA411131	288m_3_48h	Human stool ex vivo culture	288	Sample	3	48h	Maslinic acid
SA411132	489_1_0h	Human stool ex vivo culture	489	Sample	1	0h	-
SA411133	489m_1_0h	Human stool ex vivo culture	489	Sample	1	0h	Maslinic acid
SA411134	489_1_48h	Human stool ex vivo culture	489	Sample	1	48h	-
SA411135	489m_1_48h	Human stool ex vivo culture	489	Sample	1	48h	Maslinic acid
SA411136	489_2_0h	Human stool ex vivo culture	489	Sample	2	0h	-
SA411137	489m_2_0h	Human stool ex vivo culture	489	Sample	2	0h	Maslinic acid
SA411138	489_2_48h	Human stool ex vivo culture	489	Sample	2	48h	-
SA411139	489m_2_48h	Human stool ex vivo culture	489	Sample	2	48h	Maslinic acid
SA411140	489_3_0h	Human stool ex vivo culture	489	Sample	3	0h	-
SA411141	489m_3_0h	Human stool ex vivo culture	489	Sample	3	0h	Maslinic acid
SA411142	489_3_48h	Human stool ex vivo culture	489	Sample	3	48h	-
SA411143	489m_3_48h	Human stool ex vivo culture	489	Sample	3	48h	Maslinic acid
SA411144	619_1_0h	Human stool ex vivo culture	619	Sample	1	0h	-
SA411145	619m_1_0h	Human stool ex vivo culture	619	Sample	1	0h	Maslinic acid
SA411146	619_1_48h	Human stool ex vivo culture	619	Sample	1	48h	-
SA411147	619m_1_48h	Human stool ex vivo culture	619	Sample	1	48h	Maslinic acid
SA411148	619_2_0h	Human stool ex vivo culture	619	Sample	2	0h	-
SA411149	619m_2_0h	Human stool ex vivo culture	619	Sample	2	0h	Maslinic acid
SA411150	619_2_48h	Human stool ex vivo culture	619	Sample	2	48h	-
SA411151	619m_2_48h	Human stool ex vivo culture	619	Sample	2	48h	Maslinic acid
SA411152	619_3_0h	Human stool ex vivo culture	619	Sample	3	0h	-
SA411153	619m_3_0h	Human stool ex vivo culture	619	Sample	3	0h	Maslinic acid
SA411154	619_3_48h	Human stool ex vivo culture	619	Sample	3	48h	-
SA411155	619m_3_48h	Human stool ex vivo culture	619	Sample	3	48h	Maslinic acid
SA411156	745_1_0h	Human stool ex vivo culture	745	Sample	1	0h	-
SA411157	745m_1_0h	Human stool ex vivo culture	745	Sample	1	0h	Maslinic acid
SA411158	745_1_48h	Human stool ex vivo culture	745	Sample	1	48h	-
SA411159	745m_1_48h	Human stool ex vivo culture	745	Sample	1	48h	Maslinic acid
SA411160	745_2_0h	Human stool ex vivo culture	745	Sample	2	0h	-
SA411161	745m_2_0h	Human stool ex vivo culture	745	Sample	2	0h	Maslinic acid
SA411162	745_2_48h	Human stool ex vivo culture	745	Sample	2	48h	-
SA411163	745m_2_48h	Human stool ex vivo culture	745	Sample	2	48h	Maslinic acid
SA411164	745_3_0h	Human stool ex vivo culture	745	Sample	3	0h	-
SA411165	745m_3_0h	Human stool ex vivo culture	745	Sample	3	0h	Maslinic acid
SA411166	745_3_48h	Human stool ex vivo culture	745	Sample	3	48h	-
SA411167	745m_3_48h	Human stool ex vivo culture	745	Sample	3	48h	Maslinic acid
SA411168	med_1_0h	Media used for stool cultures	None	Sample	1	0h	-
SA411169	medM_1_0h	Media used for stool cultures	None	Sample	1	0h	Maslinic acid
SA411170	med_1_48h	Media used for stool cultures	None	Sample	1	48h	-
SA411171	medM_1_48h	Media used for stool cultures	None	Sample	1	48h	Maslinic acid
SA411172	med_2_0h	Media used for stool cultures	None	Sample	2	0h	-
SA411173	medM_2_0h	Media used for stool cultures	None	Sample	2	0h	Maslinic acid
SA411174	med_2_48h	Media used for stool cultures	None	Sample	2	48h	-
SA411175	medM_2_48h	Media used for stool cultures	None	Sample	2	48h	Maslinic acid
SA411176	med_3_0h	Media used for stool cultures	None	Sample	3	0h	-
SA411177	medM_3_0h	Media used for stool cultures	None	Sample	3	0h	Maslinic acid
SA411178	med_3_48h	Media used for stool cultures	None	Sample	3	48h	-
SA411179	medM_3_48h	Media used for stool cultures	None	Sample	3	48h	Maslinic acid
SA411180	PREFA01	Quality control pool	-	QC-drift_correction	PREFA01	PREFA01	-
SA411181	PREFA02	Quality control pool	-	QC-drift_correction	PREFA02	PREFA02	-
SA411182	PREFA03	Quality control pool	-	QC-drift_correction	PREFA03	PREFA03	-
SA411183	PREFA04	Quality control pool	-	QC-drift_correction	PREFA04	PREFA04	-
SA411184	PREFB01	Quality control pool	-	QC-pooled_ref	PREFB01	PREFB01	-
SA411185	PREFB02	Quality control pool	-	QC-pooled_ref	PREFB02	PREFB02	-
SA411186	PREFB03	Quality control pool	-	QC-pooled_ref	PREFB03	PREFB03	-
SA411187	PREFB04	Quality control pool	-	QC-pooled_ref	PREFB04	PREFB04	-
SA411188	Titration-100	Titration of Quality control pool	-	Titration	Titration-100	Titration-100	-
SA411189	Titration-10	Titration of Quality control pool	-	Titration	Titration-10	Titration-10	-
SA411190	Titration-20	Titration of Quality control pool	-	Titration	Titration-20	Titration-20	-
SA411191	Titration-40	Titration of Quality control pool	-	Titration	Titration-40	Titration-40	-
SA411192	Titration-60	Titration of Quality control pool	-	Titration	Titration-60	Titration-60	-
SA411193	Titration-80	Titration of Quality control pool	-	Titration	Titration-80	Titration-80	-

Showing results 1 to 74 of 74

Showing results 1 to 74 of 74

Collection:

Collection ID:	CO003913
Collection Summary:	Stool samples were collected (250-1,000 mg of stool) from healthy human donors and immediately frozen once at -80°C after collection.
Sample Type:	Feces
Collection Frequency:	Once
Volumeoramount Collected:	250-1,000 mg of stool
Storage Conditions:	-80℃
Additives:	None

Treatment:

Treatment ID:	TR003929
Treatment Summary:	Frozen stool was thawed and homogenized in 10 mL sterile phosphate buffered saline containing 40% glycerol and 0.001% cysteine using GentleMACS Dissaciator, and stored at -80°C. Homogenized stool was thawed and diluted in rich defined media, RDM, (6% stool, 94% RDM). RDM was prepared by combining 62.5 mL of 4X MM Salts (pH 7.2) with 0.5 g of glucose, 0.25 g each of cellobiose, maltose, and fructose, and 0.125 g of cysteine (free base) in a total volume of 250 mL. Additionally, 50 mL of 5X Amino Acid Mix (Teknova) and 25 mL of 10X Nucleotide Mix (Teknova) were added. Supplementation included 2.5 mL each of ATCC Trace Mineral Supplement and ATCC Vitamin Supplement. To further enhance the medium, 25 µL of 50 mg/mL heme in 0.1 M NaOH, 25 µL of 10 mg/mL vitamin K in ethanol, 250 µL of sterile 0.1 M MgCl₂ solution, 250 µL of sterile 0.4 mg/mL FeSO₄, 250 µL of sterile 0.8% CaCl₂, and 125 µL of sterile 0.01 mg/mL vitamin B₁₂ were incorporated. The final volume was adjusted to 250 mL with sterile water (106 mL).

Treatment ID:

TR003929

Treatment Summary:

Frozen stool was thawed and homogenized in 10 mL sterile phosphate buffered saline containing 40% glycerol and 0.001% cysteine using GentleMACS Dissaciator, and stored at -80°C. Homogenized stool was thawed and diluted in rich defined media, RDM, (6% stool, 94% RDM). RDM was prepared by combining 62.5 mL of 4X MM Salts (pH 7.2) with 0.5 g of glucose, 0.25 g each of cellobiose, maltose, and fructose, and 0.125 g of cysteine (free base) in a total volume of 250 mL. Additionally, 50 mL of 5X Amino Acid Mix (Teknova) and 25 mL of 10X Nucleotide Mix (Teknova) were added. Supplementation included 2.5 mL each of ATCC Trace Mineral Supplement and ATCC Vitamin Supplement. To further enhance the medium, 25 µL of 50 mg/mL heme in 0.1 M NaOH, 25 µL of 10 mg/mL vitamin K in ethanol, 250 µL of sterile 0.1 M MgCl₂ solution, 250 µL of sterile 0.4 mg/mL FeSO₄, 250 µL of sterile 0.8% CaCl₂, and 125 µL of sterile 0.01 mg/mL vitamin B₁₂ were incorporated. The final volume was adjusted to 250 mL with sterile water (106 mL).

Sample Preparation:

Sampleprep ID:	SP003926
Sampleprep Summary:	LC–MS samples were prepared from ex vivo stool culture samples for each profiling method as follows: - HILIC-pos: Samples (10 μL) were extracted with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000g, 4°C), and the supernatants (10 μL) injected directly onto column. - C8-pos: Samples (10 μL) were extracted using 190 μL isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000g, ambient temperature), supernatants (2 μL) were injected directly onto column. - C18-neg: Samples (30 μl) were extracted using 90 μL methanol containing 15R-15-methyl ProstaglandinA2,15R-15-methyl ProstaglandinF2α, 15S-15-methyl ProstaglandinD2, 15S-15-methyl ProstaglandinE1, and 15S-15-methyl Prostaglandin E2 as internal standards (Cayman Chemical Co.) and centrifuged (10 min, 9,000g, 4°C). The supernatants (10 μL) were injected onto column. - HILIC-neg: Samples (30 μL) were extracted with the addition of four volumes of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000g, 4°C) and the supernatants 10 μL) were injected directly onto column.

Sampleprep ID:

SP003926

Sampleprep Summary:

LC–MS samples were prepared from ex vivo stool culture samples for each profiling method as follows: - HILIC-pos: Samples (10 μL) were extracted with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000g, 4°C), and the supernatants (10 μL) injected directly onto column. - C8-pos: Samples (10 μL) were extracted using 190 μL isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000g, ambient temperature), supernatants (2 μL) were injected directly onto column. - C18-neg: Samples (30 μl) were extracted using 90 μL methanol containing 15R-15-methyl ProstaglandinA2,15R-15-methyl ProstaglandinF2α, 15S-15-methyl ProstaglandinD2, 15S-15-methyl ProstaglandinE1, and 15S-15-methyl Prostaglandin E2 as internal standards (Cayman Chemical Co.) and centrifuged (10 min, 9,000g, 4°C). The supernatants (10 μL) were injected onto column. - HILIC-neg: Samples (30 μL) were extracted with the addition of four volumes of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000g, 4°C) and the supernatants 10 μL) were injected directly onto column.

Chromatography:

Chromatography ID:	CH004717
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters ACQUITY UPLC BEH C18 (150 x 1.7 mm, 2.1 µm)
Column Temperature:	45°C
Flow Gradient:	The column was eluted isocratically at a flow rate of 450 µL/min with 20% mobile phase A for 3 minutes followed by a linear gradient to 100% mobile phase B over 12 minutes.
Flow Rate:	450 µL/min
Solvent A:	100% Water; 0.01% Formic acid
Solvent B:	100% Acetonitrile; 0.01% Acetic acid
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN006221
Analysis Type:	MS
Chromatography ID:	CH004717
Num Factors:	74
Num Metabolites:	104
Has Mz:	1
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003786_AN006221_Results.txt
Units:	Abudances