Summary of Study ST000422

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 IDST000422
Study TitleType 1 Diabetes good glycemic control and controls 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 Date2016-07-01
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:SU000443
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
SA02135708feb12_56-r002.dND
SA02135808feb12_80-r001.dND
SA02135908feb12_56-r001.dND
SA02136008feb12_45-r001.dND
SA02136108feb12_43-r002.dND
SA02136208feb12_80-r002.dND
SA02136308feb12_45-r002.dND
SA02136408feb12_59-r001.dND
SA02136508feb12_62-r001.dND
SA02136608feb12_62-r002.dND
SA02136708feb12_81-r002.dND
SA02136808feb12_81-r001.dND
SA02136908feb12_59-r002.dND
SA02137008feb12_43-r001.dND
SA02137108feb12_39-r002.dND
SA02137208feb12_22-r002.dND
SA02137308feb12_24-r001.dND
SA02137408feb12_22-r001.dND
SA02137508feb12_15-r002.dND
SA02137608feb12_13-r002.dND
SA02137708feb12_15-r001.dND
SA02137808feb12_24-r002.dND
SA02137908feb12_26-r001.dND
SA02138008feb12_39-r001.dND
SA02138115feb12_13-r002.dND
SA02138208feb12_28-r002.dND
SA02138308feb12_28-r001.dND
SA02138408feb12_26-r002.dND
SA02138508feb12_41-r002.dND
SA02138615feb12_22-r002.dND
SA02138713feb12_39-r002.dND
SA02138813feb12_41-r002.dND
SA02138913feb12_28-r002.dND
SA02139013feb12_26-r002.dND
SA02139113feb12_22-r002.dND
SA02139213feb12_24-r002.dND
SA02139313feb12_43-r002.dND
SA02139413feb12_45-r002.dND
SA02139513feb12_81-r002.dND
SA02139613feb12_62-r002.dND
SA02139713feb12_59-r002.dND
SA02139813feb12_80-r002.dND
SA02139913feb12_56-r002.dND
SA02140013feb12_15-r002.dND
SA02140113feb12_13-r002.dND
SA02140215feb12_39-r002.dND
SA02140315feb12_41-r002.dND
SA02140415feb12_28-r002.dND
SA02140515feb12_26-r002.dND
SA02140608feb12_13-r001.dND
SA02140715feb12_24-r002.dND
SA02140815feb12_43-r002.dND
SA02140915feb12_45-r002.dND
SA02141015feb12_81-r002.dND
SA02141115feb12_62-r002.dND
SA02141215feb12_59-r002.dND
SA02141315feb12_80-r002.dND
SA02141415feb12_56-r002.dND
SA02141515feb12_15-r002.dND
SA02141608feb12_41-r001.dND
SA02141710jan12_80-r002.dND
SA02141810jan12_22-r002.dND
SA02141910jan12_43-r002.dND
SA02142010jan12_43-r001.dND
SA02142110jan12_22-r001.dND
SA02142210jan12_28-r002.dND
SA02142310jan12_26-r001.dND
SA02142410jan12_28-r001.dND
SA02142510jan12_80-r001.dND
SA02142610jan12_39-r002.dND
SA02142710jan12_26-r002.dND
SA02142810jan12_45-r001.dND
SA02142910jan12_45-r002.dND
SA02143010jan12_56-r001.dND
SA02143110jan12_56-r002.dND
SA02143210jan12_24-r001.dND
SA02143310jan12_24-r002.dND
SA02143410jan12_59-r002.dND
SA02143510jan12_59-r001.dND
SA02143610jan12_41-r001.dND
SA02143710jan12_13-r002.dND
SA02143810jan12_81-r002.dND
SA02143910jan12_13-r001.dND
SA02144010jan12_39-r001.dND
SA02144110jan12_81-r001.dND
SA02144210jan12_15-r001.dND
SA02144310jan12_15-r002.dND
SA02144410jan12_62-r001.dND
SA02144510jan12_41-r002.dND
SA02144610jan12_62-r002.dND
SA02144715feb12_58-r002.dT1D good glycemic control
SA02144815feb12_60-r002.dT1D good glycemic control
SA02144915feb12_27-r002.dT1D good glycemic control
SA02145015feb12_38-r002.dT1D good glycemic control
SA02145115feb12_40-r002.dT1D good glycemic control
SA02145210jan12_38-r001.dT1D good glycemic control
SA02145315feb12_55-r002.dT1D good glycemic control
SA02145415feb12_44-r002.dT1D good glycemic control
SA02145510jan12_27-r002.dT1D good glycemic control
SA02145615feb12_42-r002.dT1D good glycemic control
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 180

Collection:

Collection ID:CO000437
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:TR000457
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:SP000450
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 AN000667 AN000668 AN000669 AN000670
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:CH000482
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:CH000483
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:MS000593
Analysis ID:AN000667
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:MS000594
Analysis ID:AN000668
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:MS000595
Analysis ID:AN000669
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:MS000596
Analysis ID:AN000670
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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