Summary of Study ST000421

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

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 IDST000421
Study TitleType 1 Diabetes poor glycemic control versus control samples
Study TypePlasma metabolites in T1 diabetes
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 Date2016-07-15
Raw Data AvailableYes
Raw Data File Type(s)d
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

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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:SU000442
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
SA02113516feb12_51-r001.dND
SA02113616feb12_51-r002.dND
SA02113726mar12_38-r001.dND
SA02113826mar12_26-r002.dND
SA02113926mar12_24-r002.dND
SA02114016feb12_50-r001.dND
SA02114126mar12_24-r001.dND
SA02114226mar12_38-r002.dND
SA02114326mar12_26-r001.dND
SA02114426mar12_40-r001.dND
SA02114526mar12_44-r002.dND
SA02114616feb12_53-r001.dND
SA02114716feb12_53-r002.dND
SA02114826mar12_44-r001.dND
SA02114926mar12_42-r002.dND
SA02115026mar12_40-r002.dND
SA02115126mar12_42-r001.dND
SA02115209feb12_57-r001.dND
SA02115309feb12_56-r002.dND
SA02115423mar12_42-r002.dND
SA02115523mar12_44-r001.dND
SA02115623mar12_44-r002.dND
SA02115723mar12_42-r001.dND
SA02115823mar12_40-r002.dND
SA02115923mar12_38-r002.dND
SA02116023mar12_40-r001.dND
SA02116109feb12_53-r001.dND
SA02116209feb12_53-r002.dND
SA02116309feb12_55-r001.dND
SA02116409feb12_55-r002.dND
SA02116509feb12_56-r001.dND
SA02116623mar12_57-r002.dND
SA02116723mar12_57-r001.dND
SA02116809feb12_54-r001.dND
SA02116909feb12_54-r002.dND
SA02117016feb12_54-r001.dND
SA02117126mar12_57-r001.dND
SA02117214feb12_53-r001.dND
SA02117314feb12_53-r002.dND
SA02117414feb12_54-r001.dND
SA02117527mar12_44-r002.dND
SA02117627mar12_42-r002.dND
SA02117727mar12_40-r001.dND
SA02117827mar12_40-r002.dND
SA02117927mar12_42-r001.dND
SA02118014feb12_54-r002.dND
SA02118127mar12_57-r001.dND
SA02118214feb12_56-r002.dND
SA02118314feb12_57-r001.dND
SA02118414feb12_57-r002.dND
SA02118514feb12_56-r001.dND
SA02118614feb12_55-r002.dND
SA02118727mar12_57-r002.dND
SA02118814feb12_55-r001.dND
SA02118927mar12_38-r002.dND
SA02119027mar12_38-r001.dND
SA02119116feb12_56-r001.dND
SA02119216feb12_56-r002.dND
SA02119316feb12_57-r001.dND
SA02119416feb12_55-r002.dND
SA02119516feb12_55-r001.dND
SA02119623mar12_38-r001.dND
SA02119726mar12_57-r002.dND
SA02119816feb12_57-r002.dND
SA02119914feb12_50-r001.dND
SA02120027mar12_26-r002.dND
SA02120114feb12_51-r001.dND
SA02120214feb12_51-r002.dND
SA02120327mar12_26-r001.dND
SA02120427mar12_24-r002.dND
SA02120514feb12_50-r002.dND
SA02120627mar12_24-r001.dND
SA02120716feb12_54-r002.dND
SA02120809feb12_57-r002.dND
SA02120921mar12_42-r002.dND
SA02121009feb12_50-r002.dND
SA02121121mar12_38-r001.dND
SA02121213jan12_55-r001.dND
SA02121321mar12_26-r002.dND
SA02121413jan12_54-r002.dND
SA02121523mar12_24-r001.dND
SA02121621mar12_26-r001.dND
SA02121721mar12_40-r002.dND
SA02121809feb12_50-r001.dND
SA02121921mar12_57-r002.dND
SA02122013jan12_51-r002.dND
SA02122113jan12_57-r002.dND
SA02122213jan12_57-r001.dND
SA02122313jan12_51-r001.dND
SA02122421mar12_57-r001.dND
SA02122521mar12_42-r001.dND
SA02122623mar12_24-r002.dND
SA02122713jan12_56-r002.dND
SA02122813jan12_55-r002.dND
SA02122909feb12_51-r001.dND
SA02123021mar12_44-r002.dND
SA02123113jan12_53-r001.dND
SA02123209feb12_51-r002.dND
SA02123321mar12_40-r001.dND
SA02123413jan12_50-r001.dND
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 222

Collection:

Collection ID:CO000436
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:TR000456
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:SP000449
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 AN000663 AN000664 AN000665 AN000666
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Agilent 6220 Agilent 6220 Agilent 6220 Agilent 6220
Column None None None None
MS Type ESI ESI ESI ESI
MS instrument type TOF TOF TOF TOF
MS instrument name Agilent 6220 TOF Agilent 6220 TOF Agilent 6220 TOF Agilent 6220 TOF
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units intensity intensity intensity intensity

Chromatography:

Chromatography ID:CH000480
Chromatography Summary:The liquid chromatography platform consisted of an Acquity UPLC system (Waters, Milford, MA). Plasma metabolite separation was achieved using both hydrophilic interaction chromatography (ethylene-bridged hybrid 2.1 × 150 mm, 1.7 μm; Waters) and reversed-phase liquid chromatography C18 (high-strength silica 2.1 × 150 mm, 1.8 μm; Waters). For each column, the run time was 20 min at a flow rate of 400 μL/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. Other LC parameters were injection volume 5 μL and column temperature 50°C. Each sample was injected in triplicate with blank injections between each sample. Quality controls and standards were run at the beginning and end of the sequence.
Instrument Name:Agilent 6220
Column Name:None
Column Temperature:50
Flow Gradient:0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B.
Flow Rate:400 µL/min
Solvent A:1% acetonitrile/99% water; 0.1% formic acid; 5 mM ammonium acetate
Solvent B:95% acetonitrile/5% water; 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH000481
Chromatography Summary:The liquid chromatography platform consisted of an Acquity UPLC system (Waters, Milford, MA). Plasma metabolite separation was achieved using both hydrophilic interaction chromatography (ethylene-bridged hybrid 2.1 × 150 mm, 1.7 μm; Waters) and reversed-phase liquid chromatography C18 (high-strength silica 2.1 × 150 mm, 1.8 μm; Waters). For each column, the run time was 20 min at a flow rate of 400 μL/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. Other LC parameters were injection volume 5 μL and column temperature 50°C. Each sample was injected in triplicate with blank injections between each sample. Quality controls and standards were run at the beginning and end of the sequence.
Instrument Name:Agilent 6220
Column Name:None
Column Temperature:50
Flow Gradient:0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B.
Flow Rate:400 µL/min
Solvent A:99% water/1% acetonitrile; 0.1% formic acid; 5 mM ammonium acetate
Solvent B:95% acetonitrile/5% water; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS000589
Analysis ID:AN000663
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:300°C
Capillary Voltage:3.5 kV
Fragment Voltage:150 V
Mass Accuracy:<5 parts per million and ~20000 respectively
Nebulizer:nebulizer gas 325°C
Octpole Voltage:250 V
Scan Range Moverz:50-1200
Scanning Cycle:0.5 s
Skimmer Voltage:58 V
  
MS ID:MS000590
Analysis ID:AN000664
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:300°C
Capillary Voltage:3.5 kV
Fragment Voltage:150 V
Mass Accuracy:<5 parts per million and ~20000 respectively
Nebulizer:nebulizer gas 325°C
Octpole Voltage:250 V
Scan Range Moverz:50-1200
Scanning Cycle:0.5 s
Skimmer Voltage:58 V
  
MS ID:MS000591
Analysis ID:AN000665
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:300°C
Capillary Voltage:3.5 kV
Fragment Voltage:150 V
Mass Accuracy:<5 parts per million and ~20000 respectively
Nebulizer:nebulizer gas 325°C
Octpole Voltage:250 V
Scan Range Moverz:50-1200
Scanning Cycle:0.5 s
Skimmer Voltage:58 V
  
MS ID:MS000592
Analysis ID:AN000666
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:300°C
Capillary Voltage:3.5 kV
Fragment Voltage:150 V
Mass Accuracy:<5 parts per million and ~20000 respectively
Nebulizer:nebulizer gas 325°C
Octpole Voltage:250 V
Scan Range Moverz:50-1200
Scanning Cycle:0.5 s
Skimmer Voltage:58 V
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