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MB Sample ID: SA052812
| Local Sample ID: | 79 |
| Subject ID: | SU000936 |
| Subject Type: | Human serum |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000936 |
| Subject Type: | Human serum |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 79 | SA052812 | FL010003 | Control | Type |
Collection:
| Collection ID: | CO000930 |
| Collection Summary: | Patients with confirmed UC (n = 20) were recruited from either the outpatient endoscopy unit or IBD clinic at Vanderbilt University Medical Center. Patients with confirmed CD (n = 20) were recruited from the IBD clinic at Vanderbilt University Medical Center. IBD diagnosis was determined by accepted clinical and histologic criteria by an IBD specialist. Non-IBD control subjects (n = 20) were recruited from patients undergoing colonoscopy for colorectal cancer screening or other non-IBD related indications. Individuals who were pregnant, had known coagulopathy or bleeding disorders, known renal or hepatic impairment, prior organ transplant, or were unable to give informed consent were excluded. Blood was collected in a vacutainer without additives and allowed to clot. The sample was centrifuged within an hour of collection and serum was aliquoted. Serum samples were snap frozen with dry ice and then stored at –80°C. |
| Sample Type: | Blood |
Treatment:
| Treatment ID: | TR000950 |
| Treatment Summary: | Individuals were categorized as either having Crohn disease, Ulcerative colitis, or as non-IBD controls by accepted clinical and histologic criteria by an IBD specialist. |
Sample Preparation:
| Sampleprep ID: | SP000943 |
| Sampleprep Summary: | : All samples were maintained at -80oC until processed. 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. |
| Sampleprep Protocol Filename: | SupplementalMaterial1.docx |
Combined analysis:
| Analysis ID | AN001462 | AN001463 | AN001464 | AN001465 |
|---|---|---|---|---|
| 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 BEH C18 (100 x 2.1mm,1.7um) | Waters Acquity BEH C18 (100 x 2.1mm,1.7um) | Waters Acquity BEH C18 (100 x 2.1mm,1.7um) | Waters Acquity 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 | raw area counts | raw area counts | raw area counts |
Chromatography:
| Chromatography ID: | CH001028 |
| Chromatography Summary: | 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). A 2nd 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 C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA and was operated at an overall higher organic content. A 3rd 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. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001029 |
| Chromatography Summary: | The 4th 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. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Solvent A: | 100% water; 10 mM ammonium formate, pH 10.8 |
| Solvent B: | 100% acetonitrile; 10 mM ammonium formate, pH 10.8 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001350 |
| Analysis ID: | AN001462 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Waters ACQUITY ultra-performance liquid chromatography (UPLC) 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 |
| Ion Mode: | POSITIVE |
| Resolution Setting: | 35,000 |
| MS ID: | MS001351 |
| Analysis ID: | AN001463 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Waters ACQUITY ultra-performance liquid chromatography (UPLC) 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 |
| Ion Mode: | POSITIVE |
| Resolution Setting: | 35,000 |
| MS ID: | MS001352 |
| Analysis ID: | AN001464 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Waters ACQUITY ultra-performance liquid chromatography (UPLC) 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 |
| Ion Mode: | NEGATIVE |
| Resolution Setting: | 35,000 |
| MS ID: | MS001353 |
| Analysis ID: | AN001465 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Waters ACQUITY ultra-performance liquid chromatography (UPLC) 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 |
| Ion Mode: | NEGATIVE |
| Resolution Setting: | 35,000 |
