Summary of Study ST003799

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.

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Study IDST003799
Study TitleMolecular fingerprint inference reveals bioactive lipids and microbial metabolites in colitis. Study 2.
Study TypeBacterial cell cultures
Study SummaryUntargeted 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 NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone(617) 714-1729
Submit Date2025-03-04
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-08-04
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M8653M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Factors:

Subject type: Bacteria; Subject species: Dorea longicatena (Factor headings shown in green)

mb_sample_id local_sample_id Species Media Replicate
SA416010CB-R1_CHG_24hClostridium bolteae CHG R1
SA416011CB-R1_CHG_6hClostridium bolteae CHG R1
SA416012CB-R1_CHG_48hClostridium bolteae CHG R1
SA416013CB-R2_CHG_48hClostridium bolteae CHG R2
SA416014CB-R2_CHG_24hClostridium bolteae CHG R2
SA416015CB-R2_CHG_6hClostridium bolteae CHG R2
SA416016CB-R3_CHG_24hClostridium bolteae CHG R3
SA416017CB-R3_CHG_48hClostridium bolteae CHG R3
SA416018CB-R3_CHG_6hClostridium bolteae CHG R3
SA416019CB-R1_Gifu_6hClostridium bolteae Gifu R1
SA416020CB-R1_Gifu_24hClostridium bolteae Gifu R1
SA416021CB-R1_Gifu_48hClostridium bolteae Gifu R1
SA416022CB-R2_Gifu_48hClostridium bolteae Gifu R2
SA416023CB-R2_Gifu_6hClostridium bolteae Gifu R2
SA416024CB-R2_Gifu_24hClostridium bolteae Gifu R2
SA416025CB-R3_Gifu_6hClostridium bolteae Gifu R3
SA416026CB-R3_Gifu_24hClostridium bolteae Gifu R3
SA416027CB-R3_Gifu_48hClostridium bolteae Gifu R3
SA416028CB-R1_Mega_6hClostridium bolteae Mega R1
SA416029CB-R1_Mega_24hClostridium bolteae Mega R1
SA416030CB-R1_Mega_48hClostridium bolteae Mega R1
SA416031CB-R2_Mega_6hClostridium bolteae Mega R2
SA416032CB-R2_Mega_48hClostridium bolteae Mega R2
SA416033CB-R2_Mega_24hClostridium bolteae Mega R2
SA416034CB-R3_Mega_6hClostridium bolteae Mega R3
SA416035CB-R3_Mega_24hClostridium bolteae Mega R3
SA416036CB-R3_Mega_48hClostridium bolteae Mega R3
SA416037CC-R1_CHG_24hClostridium clostridioforme CHG R1
SA416038CC-R1_CHG_48hClostridium clostridioforme CHG R1
SA416039CC-R1_CHG_6hClostridium clostridioforme CHG R1
SA416040CC-R2_CHG_24hClostridium clostridioforme CHG R2
SA416041CC-R2_CHG_48hClostridium clostridioforme CHG R2
SA416042CC-R2_CHG_6hClostridium clostridioforme CHG R2
SA416043CC-R3_CHG_24hClostridium clostridioforme CHG R3
SA416044CC-R3_CHG_48hClostridium clostridioforme CHG R3
SA416045CC-R3_CHG_6hClostridium clostridioforme CHG R3
SA416046CC-R1_Gifu_6hClostridium clostridioforme Gifu R1
SA416047CC-R1_Gifu_48hClostridium clostridioforme Gifu R1
SA416048CC-R1_Gifu_24hClostridium clostridioforme Gifu R1
SA416049CC-R2_Gifu_6hClostridium clostridioforme Gifu R2
SA416050CC-R2_Gifu_24hClostridium clostridioforme Gifu R2
SA416051CC-R2_Gifu_48hClostridium clostridioforme Gifu R2
SA416052CC-R3_Gifu_48hClostridium clostridioforme Gifu R3
SA416053CC-R3_Gifu_24hClostridium clostridioforme Gifu R3
SA416054CC-R3_Gifu_6hClostridium clostridioforme Gifu R3
SA416055CC-R1_Mega_24hClostridium clostridioforme Mega R1
SA416056CC-R1_Mega_6hClostridium clostridioforme Mega R1
SA416057CC-R1_Mega_48hClostridium clostridioforme Mega R1
SA416058CC-R2_Mega_24hClostridium clostridioforme Mega R2
SA416059CC-R2_Mega_6hClostridium clostridioforme Mega R2
SA416060CC-R2_Mega_48hClostridium clostridioforme Mega R2
SA416061CC-R3_Mega_48hClostridium clostridioforme Mega R3
SA416062CC-R3_Mega_24hClostridium clostridioforme Mega R3
SA416063CC-R3_Mega_6hClostridium clostridioforme Mega R3
SA416064CI-R1_CHG_24hClostridium innocuum CHG R1
SA416065CI-R1_CHG_6hClostridium innocuum CHG R1
SA416066CI-R1_CHG_48hClostridium innocuum CHG R1
SA416067CI-R2_CHG_6hClostridium innocuum CHG R2
SA416068CI-R2_CHG_24hClostridium innocuum CHG R2
SA416069CI-R2_CHG_48hClostridium innocuum CHG R2
SA416070CI-R3_CHG_6hClostridium innocuum CHG R3
SA416071CI-R3_CHG_48hClostridium innocuum CHG R3
SA416072CI-R3_CHG_24hClostridium innocuum CHG R3
SA416073CI-R1_Mega_24hClostridium innocuum Mega R1
SA416074CI-R1_Mega_48hClostridium innocuum Mega R1
SA416075CI-R1_Mega_6hClostridium innocuum Mega R1
SA416076CI-R2_Mega_24hClostridium innocuum Mega R2
SA416077CI-R2_Mega_48hClostridium innocuum Mega R2
SA416078CI-R2_Mega_6hClostridium innocuum Mega R2
SA416079CI-R3_Mega_48hClostridium innocuum Mega R3
SA416080CI-R3_Mega_24hClostridium innocuum Mega R3
SA416081CI-R3_Mega_6hClostridium innocuum Mega R3
SA416082CS-R1_CHG_24hClostridium symbiosum CHG R1
SA416083CS-R1_CHG_6hClostridium symbiosum CHG R1
SA416084CS-R1_CHG_48hClostridium symbiosum CHG R1
SA416085CS-R2_CHG_24hClostridium symbiosum CHG R2
SA416086CS-R2_CHG_6hClostridium symbiosum CHG R2
SA416087CS-R2_CHG_48hClostridium symbiosum CHG R2
SA416088CS-R3_CHG_24hClostridium symbiosum CHG R3
SA416089CS-R3_CHG_6hClostridium symbiosum CHG R3
SA416090CS-R3_CHG_48hClostridium symbiosum CHG R3
SA416091CS-R1_Gifu_6hClostridium symbiosum Gifu R1
SA416092CS-R1_Gifu_24hClostridium symbiosum Gifu R1
SA416093CS-R1_Gifu_48hClostridium symbiosum Gifu R1
SA416094CS-R2_Gifu_24hClostridium symbiosum Gifu R2
SA416095CS-R2_Gifu_6hClostridium symbiosum Gifu R2
SA416096CS-R2_Gifu_48hClostridium symbiosum Gifu R2
SA416097CS-R3_Gifu_6hClostridium symbiosum Gifu R3
SA416098CS-R3_Gifu_24hClostridium symbiosum Gifu R3
SA416099CS-R3_Gifu_48hClostridium symbiosum Gifu R3
SA416100CS-R1_Mega_24hClostridium symbiosum Mega R1
SA416101CS-R1_Mega_48hClostridium symbiosum Mega R1
SA416102CS-R1_Mega_6hClostridium symbiosum Mega R1
SA416103CS-R2_Mega_48hClostridium symbiosum Mega R2
SA416104CS-R2_Mega_6hClostridium symbiosum Mega R2
SA416105CS-R2_Mega_24hClostridium symbiosum Mega R2
SA416106CS-R3_Mega_6hClostridium symbiosum Mega R3
SA416107CS-R3_Mega_48hClostridium symbiosum Mega R3
SA416108CS-R3_Mega_24hClostridium symbiosum Mega R3
SA416109DL-R1_CHG_6hDorea longicatena CHG R1
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