Return to study ST002470 main page
MB Sample ID: SA247578
| Local Sample ID: | 40017 |
| Subject ID: | SU002560 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002560 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 40017 | SA247578 | FL031120 | 4 | collectionWeek |
| 40017 | SA247578 | FL031120 | inactive | PUCAI_C3_WKall |
Collection:
| Collection ID: | CO002553 |
| Collection Summary: | Pediatric UC patients (4-17 years of age) were recruited between July 2012 and April 2015 from 29 centers in the USA and Canada and monitored over the course of one year. Patients were treatment-naive at week 0 and received either 5-aminosalicylic acid (mesalamine) or oral/intravenous corticosteroids followed by mesalamine. Up to 4 samples were collected from each patient (week 0, 4, 12 and 52). In addition, metadata and clinical data were collected, including age, gender, ethnicity, treatment, Pediatric Ulcerative Colitis Activity Index (PUCAI), disease progression (colectomy and remission status) and fecal calprotectin (ELISA). Blood samples were collected Monday-Thursday and shipped on the same day (via FedEx overnight) at room temperature for next day delivery and processing by the biorepository. If samples were collected on Friday, blood tubes were stored at the collection site at 4 degrees and then shipped at room temperature on Monday (via FedEx overnight) for next day delivery and processing. Once samples were received by the Emory Biorepository, blood samples were immediately processed using the corresponding blood tube centrifugation guidelines, aliquoted, and stored at -80 degrees. Two types of blood tubes (Becton-Dickinson) were used for collection. One tube was coated with K2EDTA anticoagulant and proprietary protease inhibitor cocktail for stabilization of human plasma proteins at the point of collection. The second tube was also coated with K2EDTA anticoagulant. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002572 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP002566 |
| Sampleprep Summary: | LC-MS samples were prepared for four profiling methods from plasma samples as follows: HILIC-pos: Metabolites were extracted by adding 90 μL of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA) to a 10 μL aliquot of plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. |
Combined analysis:
| Analysis ID | AN004029 | AN004030 | AN004031 | AN004032 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | Reversed phase | HILIC | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2 mm, 3 μm) | Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) | Phenomenex Luna NH2 (150 x 2.1mm, 3um) | Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Abundance | Abundance | Abundance | Abundance |
Chromatography:
| Chromatography ID: | CH002977 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2 mm, 3 μm) |
| Column Temperature: | 30C |
| Flow Gradient: | Isocratically with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes |
| Flow Rate: | 250 µL/min |
| Solvent A: | 100% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002978 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40C |
| Flow Gradient: | The column was eluted at a flow rate of 450 µL/min isocratically for 1 minute at 80% mobile phase A, followed by a linear gradient to 80% mobile-phase B over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B. |
| Flow Rate: | 450 µL/min |
| Solvent A: | 95% water/5% methanol; 10 mM ammonium acetate; 0.1% acetic acid |
| Solvent B: | 100% methanol; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002979 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna NH2 (150 x 2.1mm, 3um) |
| Column Temperature: | 30C |
| Flow Gradient: | The column was eluted with initial conditions of 10% mobile phase A and 90% mobile phase B followed by a 10 min linear gradient to 100% mobile phase A. |
| Flow Rate: | 400 µL/min |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002980 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C18 (150 x 1.7mm,2.1um) |
| Column Temperature: | 45C |
| Flow Gradient: | The column was eluted isocratically at a flow rate of 450 µL/min with 20% mobile phase A for 3 minutes followed by a linear gradient to 100% mobile phase B over 12 minutes. |
| Flow Rate: | 450 µL/min |
| Solvent A: | 100% water; 0.01% formic acid |
| Solvent B: | 100% acetonitrile; 0.01% acetic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003776 |
| Analysis ID: | AN004029 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003777 |
| Analysis ID: | AN004030 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003778 |
| Analysis ID: | AN004031 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003779 |
| Analysis ID: | AN004032 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples. |
| Ion Mode: | NEGATIVE |
