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MB Sample ID: SA304333
Local Sample ID: | 3900089 |
Subject ID: | SU002929 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 18 and older |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002929 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 18 and older |
Gender: | Male and female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
3900089 | SA304333 | FL036651 | AASKG1 | study |
Collection:
Collection ID: | CO002922 |
Collection Summary: | samples were obtained from NIDDK repository |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR002938 |
Treatment Summary: | Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
Sample Preparation:
Sampleprep ID: | SP002935 |
Sampleprep Summary: | All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted as described below |
Combined analysis:
Analysis ID | AN004594 | AN004595 | AN004596 | AN004597 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
Units | raw area counts rescaled to set the median equal to 1 | raw area counts rescaled to set the median equal to 1 | raw area counts rescaled to set the median equal to 1 | raw area counts rescaled to set the median equal to 1 |
Chromatography:
Chromatography ID: | CH003454 |
Chromatography Summary: | Low pH polar (LC/MS Pos early) |
Instrument Name: | Waters Acquity |
Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
Column Temperature: | - |
Flow Gradient: | - |
Flow Rate: | - |
Solvent A: | - |
Solvent B: | - |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH003455 |
Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
Instrument Name: | Waters Acquity |
Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
Column Temperature: | - |
Flow Gradient: | - |
Flow Rate: | - |
Solvent A: | - |
Solvent B: | - |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH003456 |
Chromatography Summary: | High pH (LC/MS Neg) |
Instrument Name: | Waters Acquity |
Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
Column Temperature: | - |
Flow Gradient: | - |
Flow Rate: | - |
Solvent A: | - |
Solvent B: | - |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH003457 |
Chromatography Summary: | HILIC (LC/MS Polar Neg) |
Instrument Name: | Waters Acquity |
Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
Column Temperature: | - |
Flow Gradient: | - |
Flow Rate: | - |
Solvent A: | - |
Solvent B: | - |
Chromatography Type: | HILIC |
MS:
MS ID: | MS004340 |
Analysis ID: | AN004594 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Metabolon (LC/MS Pos early) |
Ion Mode: | POSITIVE |
MS ID: | MS004341 |
Analysis ID: | AN004595 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Metabolon (LC/MS Pos late) |
Ion Mode: | POSITIVE |
MS ID: | MS004342 |
Analysis ID: | AN004596 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Metabolon (LC/MS Neg) |
Ion Mode: | NEGATIVE |
MS ID: | MS004343 |
Analysis ID: | AN004597 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Metabolon (LC/MS Polar) |
Ion Mode: | NEGATIVE |