Summary of Study ST000045
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 PR000044. The data can be accessed directly via it's Project DOI: 10.21228/M8D59R This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000045 |
| Study Title | Plasma metabolomics: Comparison of non-diabetic controls with T1D patients |
| Study Type | Drug effect study |
| Study Summary | Non-diabetic controls whose metabolites were compared to T1D patients with and without insulin. Seven C-peptidenegative T1D subjects were studied on two occasions: one during insulin treatment and the other following withdrawal of insulin for 8 h and compared with matched healthy ND participants |
| Institute | Mayo Clinic |
| Department | Endocrinology |
| Last Name | Nair |
| First Name | Sreekumaran |
| Dasari.Surendra@mayo.edu | |
| Submit Date | 2014-03-24 |
| Num Groups | 1 |
| Total Subjects | 7 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 66 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2014-04-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000044 |
| Project DOI: | doi: 10.21228/M8D59R |
| Project Title: | Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes. |
| Project Type: | Untargeted LC-MS Metabolomics |
| Project Summary: | Insulin regulates many cellular processes, but the full impact of insulin deficiency on cellular functions remains to be defined. Applying a mass spectrometry-based nontargeted metabolomics approach, we report here alterations of 330 plasma metabolites representing 33 metabolic pathways during an 8-h insulin deprivation in type 1 diabetic individuals. These pathways included those known to be affected by insulin such as glucose, amino acid and lipid metabolism, Krebs cycle, and immune responses and those hitherto unknown to be altered including prostaglandin, arachidonic acid, leukotrienes, neurotransmitters, nucleotides, and anti-inflammatory responses. A significant concordance of metabolome and skeletal muscle transcriptome-based pathways supports an assumption that plasma metabolites are chemical fingerprints of cellular events. Although insulin treatment normalized plasma glucose and many other metabolites, there were 71 metabolites and 24 pathways that differed between nondiabetes and insulin-treated type 1 diabetes. Confirmation of many known pathways altered by insulin using a single blood test offers confidence in the current approach. Future research needs to be focused on newly discovered pathways affected by insulin deficiency and systemic insulin treatment to determine whether they contribute to the high morbidity and mortality in T1D despite insulin treatment. |
| Institute: | Mayo Clinic |
| Department: | Endocrinology |
| Last Name: | Nair |
| First Name: | Sreekumaran |
| Address: | 200 First Street SW, Rochester, MN 55905 |
| Email: | Dasari.Surendra@mayo.edu |
| Phone: | 507-284-0513 |
| Funding Source: | R01 DK41973, UL1 RR024150-01 |
| Project Comments: | 22415876 |
Subject:
| Subject ID: | SU000063 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA001922 | Group6B | Insulin Withdrawal |
| SA001923 | Group7B | Insulin Withdrawal |
| SA001924 | Group5B | Insulin Withdrawal |
| SA001925 | Group4B | Insulin Withdrawal |
| SA001926 | Group1B | Insulin Withdrawal |
| SA001927 | Group2B | Insulin Withdrawal |
| SA001928 | Group3B | Insulin Withdrawal |
| SA001929 | Group3C | Saline Infusion |
| SA001930 | Group2C | Saline Infusion |
| SA001931 | Group4C | Saline Infusion |
| SA001932 | Group7C | Saline Infusion |
| SA001933 | Group1C | Saline Infusion |
| SA001934 | Group6C | Saline Infusion |
| SA001935 | Group5C | Saline Infusion |
| Showing results 1 to 14 of 14 |
Collection:
| Collection ID: | CO000046 |
| Collection Summary: | Arterialized venous blood was obtained from a catheterized hand vein maintained at 60°C using a hot box for the duration of the study. Plasma samples were stored at -80°C until analysis. |
| Sample Type: | Blood. Plasma was isolated for MS analysis. |
| Collection Location: | Hand vein |
Treatment:
| Treatment ID: | TR000064 |
| Treatment Summary: | Saline Infusion | Insulin Withdrawal | Insulin Infusion |
| Treatment Protocol ID: | SI / IW / II |
| Treatment Protocol Comments: | ND participants were kept on a saline infusion from the evening following their meal. | Insulin was discontinued for 8.6 +/- 0.6 h starting at 0400 h. | Insulin was infused into a forearm vein to maintain blood glucose between 4.44 and 5.56 mmol | L overnight until 1200 h the next day. |
| Treatment Compound: | Saline | Insulin |
Sample Preparation:
| Sampleprep ID: | SP000059 |
| 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 | AN000072 | AN000073 | AN000074 | AN000075 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | HILIC | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| 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 | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Raw MS Intensities | Raw MS Intensities | Raw MS Intensities | Raw MS Intensities |
Chromatography:
| Chromatography ID: | CH000047 |
| Chromatography Summary: | C18 |
| Chromatography Comments: | 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 m; Waters) and reversed-phase liquid chromatography C18 (high-strength silica 2.1 150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/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 L and column temperature 50C. 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: | Waters Acquity |
| Column Name: | Waters high-strength silica (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000048 |
| Chromatography Summary: | HILIC |
| Chromatography Comments: | 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 m; Waters) and reversed-phase liquid chromatography C18 (high-strength silica 2.1 150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. Other LC parameters were injection volume 5 L and column temperature 50C. 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: | Waters Acquity |
| Column Name: | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000053 |
| Analysis ID: | AN000072 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Positive-ion mode/C18: A 6220 ToF MS (Agilent Technologies) was operated in both positive and negative electrospray ionization modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were <5 parts per million (ppm) and ~20,000, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000054 |
| Analysis ID: | AN000073 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Positive-ion mode/HILIC: A 6220 ToF MS (Agilent Technologies) was operated in both positive and negative electrospray ionization modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were <5 parts per million (ppm) and ~20,000, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000055 |
| Analysis ID: | AN000074 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Negative-ion mode/C18: A 6220 ToF MS (Agilent Technologies) was operated in both positive and negative electrospray ionization modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were <5 parts per million (ppm) and ~20,000, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS000056 |
| Analysis ID: | AN000075 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Negative-ion mode/HILIC: A 6220 ToF MS (Agilent Technologies) was operated in both positive and negative electrospray ionization modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were <5 parts per million (ppm) and ~20,000, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
