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MB Sample ID: SA177622
| Local Sample ID: | F_64 |
| Subject ID: | SU001992 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001992 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| F_64 | SA177622 | FL021962 | case | group |
| F_64 | SA177622 | FL021962 | F | gender |
Collection:
| Collection ID: | CO001985 |
| Collection Summary: | Fecal samples were collected at each participant's home in and placed in a plastic biohazard bag with a frozen icepack to keep the samples cold. The samples were picked up by study personnel or returned to the study clinic by the participant within 24 hours of the time the stool was collected. Stool samples were stored at the clinic site in a -200C freezer for up to one week until transfer to a -800C freezer where samples were kept until processing. |
| Sample Type: | Feces |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002004 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP001998 |
| Sampleprep Summary: | Ninety-two fecal samples (250-300 mg) were randomized and homogenized in 50:50 acetonitrile:water (5 mL/ mg fecal mass) in MagNALyser tubes with ceramic beads, using an Omni Bead Ruptor (5 meters per second, two 30-sec cycles, 15 sec dwell time in between cycles). Samples were centrifuged at 16,000 relative centrifugal force (rcf) for 15 min, the supernatant was transferred, and centrifuged again at 16,000 rcf for 5 min. Quality control (QC) samples were prepared by pooling 70 µL supernatant from each of the study samples and processed identically to the study samples. An aliquot of the supernatant (100 mL) from each sample was transferred to 2.0 mL tubes and dried overnight by SpeedVac and then reconstituted in 200 mL of reconstitution solution (95:5 water-methanol solvent containing 500 ng/ml tryptophan d-5). Samples were centrifuged at 16,000 rcf at 4°C for 4 minutes and the supernatants were transferred to autosampler vials. The study samples were randomized with interspersed QC pools before data acquisition. An injection volume of 5 mL was used for the UPLC-MS analysis. |
| Sampleprep Protocol Filename: | OA-Fecal LCMS procedures |
| Processing Method: | Extraction |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
| Sample Resuspension: | 95:5 water-methanol solvent containing 500 ng/ml tryptophan d-5 |
Combined analysis:
| Analysis ID | AN003112 |
|---|---|
| Analysis type | MS |
| Chromatography type | Unspecified |
| Chromatography system | none |
| Column | none |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Orbitrap Q-Exactive HF-X |
| Ion Mode | POSITIVE |
| Units | Normalized intensity |
Chromatography:
| Chromatography ID: | CH002297 |
| Instrument Name: | none |
| Column Name: | none |
| Column Pressure: | 6000-10000 |
| Column Temperature: | 50 |
| Flow Gradient: | Time(min) Flow Rate %A %B Curve 1. 0 0.4 99.0 1.0 5 2. 1.00 0.4 99.0 1.0 5 3. 16.00 0.4 1.0 99.0 5 4. 19.00 0.4 1.0 99.0 5 5. 19.50 0.4 99.0 1.0 5 |
| Flow Rate: | 0.4 mL/min |
| Injection Temperature: | 8 |
| Internal Standard: | Tryptophan-d5 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Analytical Time: | 22 min |
| Weak Wash Solvent Name: | 10:90 Methanol:Water with 0.1% FA solution |
| Strong Wash Solvent Name: | 75:25 2-Propanol: Water with 0.1% FA solution |
| Randomization Order: | Yes |
| Chromatography Type: | Unspecified |
MS:
| MS ID: | MS002893 |
| Analysis ID: | AN003112 |
| Instrument Name: | Orbitrap Q-Exactive HF-X |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | We used DDA mode to acquire the MS and MS/MS data. Progenesis QI was used for peak picking, alignment, and normalization. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 °C |
| Capillary Voltage: | 3.5 KV |
| Collision Energy: | 10-35, ramp |
| Collision Gas: | N2 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 325°C |
| Fragmentation Method: | CID |
| Mass Accuracy: | 5 ppm |
| Desolvation Gas Flow: | 45 |
| Desolvation Temperature: | 325°C |
