Summary of Study ST002342

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 PR001504. The data can be accessed directly via it's Project DOI: 10.21228/M88X2F 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 IDST002342
Study TitleThe gut microbiome has sexually dimorphic effects on bone tissue energy metabolism and multiscale bone quality in C57BL/6J mice
Study SummaryMale and female germ-free and conventional were euthanized at 20 weeks of age, and various tissues were obtained to assess differences in bone properties associated with microbiome status and sex. For metabolomic analyses, the humeri was obtained, bone marrow was flushed using PBS, and subchondral bone metabolites were extracted using a methanol:acetone precipitation approach. Next, samples were injected, ionized, and data was acquired using LC-MS. Data was processed and converted using MSConvert and XCMS. Following this step, metabolic phenotypes of mice that differ by microbiome status and sex were investigated using MetaboAnalyst. Differences in metabolism were related to lipid, energy, and amino acid metabolism. Specifically, females, both conventional and germ-free, had dysregulated lipid metabolism, whereas, males, both conventional and germ-free had dysregulated amino acid metabolism. Other differences detected between male and female mice that differ by germ-free status corresponded to differences in bone strength, bone marrow adiposity, and osteocyte density.
Montana State University
DepartmentMechanical & Industrial Engineering, Chemistry & Biochemistry
Last NameWelhaven
First NameHope
AddressCulbertson Hall, 100
Submit Date2022-10-19
Num Groups4
Total Subjects33
Num Males17
Num Females16
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-28
Release Version1
Hope Welhaven Hope Welhaven application/zip

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Combined analysis:

Analysis ID AN003826
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1290
Column Cogent Diamond Hydride (150 × 2.1mm,4um)
MS instrument type Single quadrupole
MS instrument name Agilent 6538 QTOF
Units Peak Intensity


MS ID:MS003568
Analysis ID:AN003826
Instrument Name:Agilent 6538 QTOF
Instrument Type:Single quadrupole
MS Comments:Data was acquired in positive mode following a 25-minute method. Following injection and acquisition, .d files were converted to .mzMLs using MSConvert (Threshold peak filter value = 1000; Peak picking = true, 1-1; 32-bit, no z-lib compression). Once .mzMLs were avaiable, XCMS was used (parameters reflected run parameters = positive mode, feature detection 15 ppm, adducts = [M+H]+, [M+Na]+