Summary of study ST000457

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 PR000353. The data can be accessed directly via it's Project DOI: 10.21228/M8DW3Q This work is supported by NIH grant, U2C- DK119886.

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Study IDST000457
Study TitleMetabolomics of Mice Cohousing and Microbiota Transfer
Study SummaryThe mice serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer.
Institute
University of North Carolina
DepartmentDiscovery-Sciences-Technology (DST)
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2016-09-01
Num Groups4
Total Subjects12
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2017-10-03
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8DW3Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000353
Project DOI:doi: 10.21228/M8DW3Q
Project Title:Metabolomics of Mice Cohousing and Microbiota Transfer
Project Summary:Metabolomics analysis was performed on twelve mice serum samples from Dr. Martin Blaser's laboratory at NYU school of medicine. Serum from week 15 mice were analyzed: (a) mice received low-dose antibiotics until week 4 (STAT), (b) mice received no antibiotics (control), (c) mice received low dose antibiotics (STAT) and then cohoused with control animals (STAT-coho), (d) mice received no antibiotics and then were cohoused with STAT animals (Control-coho). In this collaboration, we are interested in the metabolic differences among these groups.
Institute:New York University
Department: Langone Medical Center
Last Name:Blaser
First Name:Martin
Address:550 First Avenue, BCD 689, New York, NY 10016
Email:martin.blaser@nyumc.edu
Phone:646-501-4386

Subject:

Subject ID:SU000478
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Group
SA023180p180 QC2-
SA023181PBS_02-
SA023182p180 Cal6-
SA023183PBS_01-
SA023184p180 QC1-
SA023185p180 QC3-
SA023186p180 Cal1-
SA023187p180 Cal4-
SA023188p180 Cal5-
SA023189p180 Cal3-
SA023190p180 Cal2-
SA023191p180 Cal7-
SA023192PBS_03-
SA023193C94Control
SA023194C38Control
SA023195C97Control
SA023196C42Control-COHO
SA023197C36Control-COHO
SA023198C35Control-COHO
SA023202S54Stat
SA023203S104Stat
SA023204S111Stat
SA023199S60STAT-COHO
SA023200S56STAT-COHO
SA023201S58STAT-COHO
SA023205TP01Study Total Pool
SA023206TP02Study Total Pool
SA023207TP03Study Total Pool
Showing results 1 to 28 of 28

Collection:

Collection ID:CO000472
Collection Summary:Serum was collected via standard operating procedures.
Sample Type:Blood

Treatment:

Treatment ID:TR000492
Treatment Summary:STAT - low dose antibiotics until week 4 STAT-COHO -STAT treated mice were cohoused with Control mice Control-COHO - Control mice were cohoused with STAT treated mice Control – No antibiotics

Sample Preparation:

Sampleprep ID:SP000485
Sampleprep Summary:"Sample Preparation Prior to Biocrates p180 Kit Plate Analysis: Thawed serum samples were vortexed for 30 seconds. Whole study pooled QC samples were created by combining 10 µL aliquot from each of the study samples into a 2 mL LoBind eppendorf tube. This QC pooled sample was then vortexed for 30 sec. Then, three whole study pooled QC samples of 30 µL each were aliquoted into 2 mL LoBind eppendorf tubes. Study samples were generated by aliquoting 30 µL from each original sample vial into 2 mL LoBind eppendorf tubes. For extraction, 1,000 µL of cold 3:3:2 Acetonitrile:Isopropyl Alcohol:Water (v/v/v) was added to each tube and vortexed for 5 min at 4 °C. The samples were then centrifuged at 4 °C and at 14,000 rcf for 2 min. A 450 µL aliquot of the supernatant from each sample was transferred into pre-labeled 2.0 mL LoBind eppendorf tubes and stored at -80 °C. Samples were then dried on a lyophilizer overnigh. The residue was reconstituted in 30 µL of 85:15 Ethanol:Water, v/v, and vortexed. Then, the samples were centrifuged at 4 °C for 4 min at 16,000 rcf. Biocrates Plate Preparation: A Biocrates p180 kit was prepared following the AbsoluteIDQ™ p180 Kit metabolomics procedure. Briefly, an internal standard mix was added to 95 of the 96 wells. Next, zero samples, QC standards and calibration standards were added to their corresponding wells. The study samples and pooled QC Samples (20 µL) were then added to the appropriate wells and dried for 30 minutes under nitrogen flow. The plate was derivatized using a 5% phenylisothiocyanate (PITC) solution in (1:1:1) ethanol:pyridine:water (v/v/v) and, then, incubated for 20 minutes followed by a drying step under nitrogen flow. An extraction solvent (5 mM ammonium acetate in methanol) was added to all wells. The plate was then shaken and centrifuged. After centrifugation, 150 µL was removed and transferred to a second 96-well plate (LCMS plate). This second plate was diluted with 150 µL of HPLC grade water for a subsequent LCMS (MRM analysis) for measuring amino acids and biogenic amines. All wells in the original plate were diluted with 400 µL of flow injection analysis (FIA) Running Solvent for a FIA-MS (MRM analysis) for measuring lipids, acylcarnitines, and hexose.

Combined analysis:

Analysis ID AN000716 AN000717 AN000718
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 1100 Agilent 1100 Agilent 1100
Column Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um)
MS Type ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex API 4000 QTrap ABI Sciex API 4000 QTrap ABI Sciex API 4000 QTrap
Ion Mode POSITIVE POSITIVE NEGATIVE
Units Intensity Intensity Intensity

Chromatography:

Chromatography ID:CH000515
Instrument Name:Agilent 1100
Column Name:Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS000636
Analysis ID:AN000716
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000637
Analysis ID:AN000717
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000638
Analysis ID:AN000718
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
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