Summary of Study ST000432

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 PR000330. The data can be accessed directly via it's Project DOI: 10.21228/M8W02Q This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files
Study IDST000432
Study TitleQuantitative measurements of vitamin D in T1D poor control, good control, and controls.
Study TypeQuantitative measurements of vitamin D
Study SummaryThe objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Institute
Mayo Clinic
DepartmentEndocrinology
LaboratoryMayo Clinic Metabolomics Resource Core
Last NameNair
First NameSreekumaran
Address200 First Street SW, Rochester, MN 55905
EmailNair.K@mayo.edu
Phone507-285-2415
Submit Date2016-07-29
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2016-09-23
Release Version1
Sreekumaran Nair Sreekumaran Nair
https://dx.doi.org/10.21228/M8W02Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000330
Project DOI:doi: 10.21228/M8W02Q
Project Title:Impact of Long-Term Poor and Good Glycemic Control on Metabolomics Alterations in Type 1 Diabetic People.
Project Type:Untargeted LC-MS Metabolomics
Project Summary:The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Institute:Mayo Clinic
Department:Endocrinology
Laboratory:Mayo Clinic Metabolomics Resource Core
Last Name:Nair
First Name:Sreekumaran
Address:200 First Street SW, Rochester, MN 55905
Email:Nair.K@mayo.edu
Phone:507-285-2415

Subject:

Subject ID:SU000453
Subject Type:Animal
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id treatment
SA021690sample43ND
SA021691sample18ND
SA021692sample6ND
SA021693sample10ND
SA021694sample41ND
SA021695sample16ND
SA021696sample24ND
SA021697sample2ND
SA021698sample36ND
SA021699sample30ND
SA021700sample4ND
SA021701sample28ND
SA021702sample40ND
SA021703sample34ND
SA021704sample32ND
SA021705sample39ND
SA021706sample42ND
SA021707sample12ND
SA021708sample20ND
SA021709sample22ND
SA021710sample8ND
SA021711sample38ND
SA021712sample26ND
SA021713sample14ND
SA021714sample35ND
SA021715sample23T1D good glycemic control
SA021716sample5T1D good glycemic control
SA021717sample1T1D good glycemic control
SA021718sample7T1D good glycemic control
SA021719sample21T1D good glycemic control
SA021720sample25T1D good glycemic control
SA021721sample17T1D good glycemic control
SA021722sample9T1D good glycemic control
SA021723sample3T1D good glycemic control
SA021724sample15T1D good glycemic control
SA021725sample19T1D good glycemic control
SA021726sample29T1D good glycemic control
SA021727sample13T1D good glycemic control
SA021728sample11T1D good glycemic control
SA021729sample27T1D good glycemic control
SA021730sample56T1D poor glycemic control
SA021731sample58T1D poor glycemic control
SA021732sample51T1D poor glycemic control
SA021733sample53T1D poor glycemic control
SA021734sample55T1D poor glycemic control
SA021735sample54T1D poor glycemic control
SA021736sample47T1D poor glycemic control
SA021737sample50T1D poor glycemic control
SA021738sample52T1D poor glycemic control
SA021739sample49T1D poor glycemic control
SA021740sample57T1D poor glycemic control
SA021741sample45T1D poor glycemic control
SA021742sample46T1D poor glycemic control
SA021743sample48T1D poor glycemic control
Showing results 1 to 54 of 54

Collection:

Collection ID:CO000447
Collection Summary:At 5:00 AM after an overnight fast, baseline blood samples were collected from study participants. Plasma samples were stored at 80°C until analysis.
Sample Type:Blood. Plasma was isolated for MS analysis.

Treatment:

Treatment ID:TR000467
Treatment Summary:Participants were admitted to the Clinical Research Unit at St Mary’s Hospital (Rochester, Minnesota) the evening before the study and spent overnight in the Clinical Research Unit. The participants were given a standard meal on the evening of the admission after which they fasted overnight. Participants with T1D were treated with insulin as per their usual individual programs. At 5:00 AM after an overnight fast, baseline blood samples were collected from study participants. Plasma samples were stored at 80°C until analysis.

Sample Preparation:

Sampleprep ID:SP000460
Sampleprep Summary:Plasma quality-control samples used in the study were prepared from pooled plasma spiked with a selection of metabolites to mimic elevated levels of metabolites during I− (insulin withdrawn) condition. Plasma was spiked with a standard mixture (3:1 ratio of plasma to spiking solution) containing 100 μg/mL niacin, hypoxanthine, leucine, isoleucine, phenylalanine, tryptophan, citric acid, glucose, hippuric acid, and taurocholic acid dissolved in 1:1 acetonitrile/water. All plasma samples (200 μL) were thawed on ice at 4°C followed by deproteinization with methanol (1:4 ratio of plasma to methanol) and vortexed for 10 s, followed by incubation at −20°C for 2 h. The samples were then centrifuged at 15,871g for 30 min at 4°C. The supernatants were lyophilized (Savant, Holbrook, NY) and stored at −20°C prior to analysis. The samples were reconstituted in 50% H2O/acetonitrile and passed through a Microcon YM3 filter (Millipore Corporation). The supernatants were transferred to analytical vials, stored in the autosampler at 4°C, and analyzed within 48 h of reconstitution in buffer.

Combined analysis:

Analysis ID AN000682
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo TSQ Quantum Ultra
Column Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Thermo Quantum Ultra
Ion Mode POSITIVE
Units ng/mL

Chromatography:

Chromatography ID:CH000494
Chromatography Summary:Plasma samples and amino acid calibration standards were prepared with MassTrak Amino Acid Analysis Solution (AAA) kit from Waters according to instructions with slight modifications for detection on a mass spectrometer. A 10 point standard concentration curve was made from the calibration standard solution to calculate amino acid concentrations in plasma samples. A solution containing U-13C4-L-aspartic acid, U-13C3-L-alanine, U-13C4-L-threonine, U-13C5-L-proline, U-13C5-L-valine, U-13C6-leucine, U-13C6-phenylalanine all from Cambridge Isotope Laboratories, 13C6-tyrosine from Isotec, L-arginine (15N2, 2H2) from MassTrace, norvaline from Sigma dissolved in 0.01N HCl was used as the internal standard solution. Frozen plasma samples were thawed, spiked with internal standard then deproteinized with cold MeOH followed by centrifugation at 10,000 g for 5 minutes prior to derivatization according to MassTrak instructions. The amino acid derivatizing reagent used was 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. High resolution separation was done using an Acquity UPLC system, injecting 1 µl of derviatized solution, with a UPLC BEH C18 1.7 micron 2.1×150 mm column from Waters. Column flow was set to 400 µl/min with a gradient from 99.9%A to 98%B where buffer A is 1% acetonitrile in 0.1% formic acid and buffer B is 100% acetonitrile. A column temp of 43 degrees Celsius and a sample tray temp of 6% Celsius. Mass detection was completed on a TSQ Ultra Quantum from Thermo Finnigan running in ESI positive mode. A scan width of 0.002, scan time of 0.04 seconds per transition mass, collision energy of 25, collision gas pressure of 1.5 mTorr, tube lens value set to 90, monitoring a signature ion of the derivitized amines at m/z 171.04 by selected reaction monitoring.
Instrument Name:Thermo TSQ Quantum Ultra
Column Name:Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
Column Temperature:43
Flow Gradient:from 99.9%A to 98%B
Flow Rate:400 µl/min
Solvent A:99% water/1% acetonitrile; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS000608
Analysis ID:AN000682
Instrument Name:Thermo Quantum Ultra
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  logo