Summary of Study ST002409

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001549. The data can be accessed directly via it's Project DOI: 10.21228/M8G99R This work is supported by NIH grant, U2C- DK119886.


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 IDST002409
Study TitleSpatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP positive data)
Study SummaryMost utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.
University of California, Davis
Last NameFolz
First NameJake
Address1 Shields Ave
Submit Date2022-12-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-01-04
Release Version1
Jake Folz Jake Folz application/zip

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Combined analysis:

Analysis ID AN003926
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column CSH C18 column (100 mm length × 2.1 mm i.d.; 1.7-µm particle size)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap
Units peak height


MS ID:MS003664
Analysis ID:AN003926
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Comments:HESI source conditions are as follows: sheath gas flow 55, auxiliary gas flow 15, sweep gas flow 3, capillary temperature 275°C, S-lens RF level 50, auxiliary gas heater temperature 450 °C, and needle voltage 3500 V and -3500 V for positive and negative ionization mode, respectively. DDA MS/MS spectra were acquired for the top 4 ions. MS scans were collected with 60k resolving power from 120-1700 m/z, AGC target of 106 ions, and maximum accumulation time of 100 ms. MS/MS spectra were collected with 15k resolving power, 1 Da isolation window, normalized collision energy of 20, 30, 60, 2 s dynamic exclusion window, 8×103 AGC target, and 50 ms maximum accumulation time. Spectra were stored in centroid mode. Three rounds of iterative exclusion MS/MS were acquired for each pooled QC sample.