Summary of Study ST000435

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


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Study IDST000435
Study TitleQuantitative measurements of amino acids in T1D poor control, good control, and controls.
Study TypeQuantitative measurements of amino acid
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.
Mayo Clinic
LaboratoryMayo Clinic Metabolomics Resource Core
Last NameNair
First NameSreekumaran
Address200 First Street SW, Rochester, MN 55905
Submit Date2016-07-20
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2016-09-23
Release Version1
Sreekumaran Nair Sreekumaran Nair application/zip

Select appropriate tab below to view additional metadata details:


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
Laboratory:Mayo Clinic Metabolomics Resource Core
Last Name:Nair
First Name:Sreekumaran
Address:200 First Street SW, Rochester, MN 55905


Subject ID:SU000456
Subject Type:Animal
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human


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

mb_sample_id local_sample_id treatment
SA021891sample32T1D good glycemic control
SA021892sample48T1D good glycemic control
SA021893sample42T1D good glycemic control
SA021894sample34T1D good glycemic control
SA021895sample36T1D good glycemic control
SA021896sample47T1D good glycemic control
SA021897sample38T1D good glycemic control
SA021898sample30T1D good glycemic control
SA021899sample45T1D good glycemic control
SA021900sample22T1D good glycemic control
SA021901sample24T1D good glycemic control
SA021902sample44T1D good glycemic control
SA021903sample28T1D good glycemic control
SA021904sample40T1D good glycemic control
SA021905sample26T1D good glycemic control
SA021906sample2T1D poor glycemic control
SA021907sample6T1D poor glycemic control
SA021908sample4T1D poor glycemic control
SA021909sample10T1D poor glycemic control
SA021910sample20T1D poor glycemic control
SA021911sample19T1D poor glycemic control
SA021912sample15T1D poor glycemic control
SA021913sample17T1D poor glycemic control
SA021914sample21T1D poor glycemic control
SA021915sample14T1D poor glycemic control
SA021916sample16T1D poor glycemic control
SA021917sample12T1D poor glycemic control
SA021918sample1T1D poor glycemic control
SA021919sample8T1D poor glycemic control
Showing results 1 to 49 of 49


Collection ID:CO000450
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 ID:TR000470
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:SP000463
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 AN000685
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 instrument type Triple quadrupole
MS instrument name Thermo Quantum Ultra
Units micromolar


Chromatography ID:CH000497
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 ID:MS000611
Analysis ID:AN000685
Instrument Name:Thermo Quantum Ultra
Instrument Type:Triple quadrupole