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MB Sample ID: SA051167
| Local Sample ID: | S8 |
| Subject ID: | SU000916 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 13 - 66 |
| Gender: | Female and Male |
| Human Inclusion Criteria: | Retrospective serum samples from leprosy patients diagnosed or not with type 1 reaction that were not receiving multidrug therapy or corticosteroid therapy at the time of blood collection. |
| Human Exclusion Criteria: | Retrospective serum samples from leprosy patients that were under multidrug therapy and/or corticosteroid therapy at the time of blood collection were excluded from the study. |
| Subject Comments: | The patients exhibited borderline tuberculoid, borderline borderline and borderline lepromatous forms of leprosy and was diagnosed or not with type 1 reaction. |
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Subject:
| Subject ID: | SU000916 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 13 - 66 |
| Gender: | Female and Male |
| Human Inclusion Criteria: | Retrospective serum samples from leprosy patients diagnosed or not with type 1 reaction that were not receiving multidrug therapy or corticosteroid therapy at the time of blood collection. |
| Human Exclusion Criteria: | Retrospective serum samples from leprosy patients that were under multidrug therapy and/or corticosteroid therapy at the time of blood collection were excluded from the study. |
| Subject Comments: | The patients exhibited borderline tuberculoid, borderline borderline and borderline lepromatous forms of leprosy and was diagnosed or not with type 1 reaction. |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S8 | SA051167 | FL009853 | Yes | Type 1 reaction (T1R) |
Collection:
| Collection ID: | CO000910 |
| Collection Summary: | The whole blood (10 mL) was collected in a Vacutainer tube from Becton Dickinson (BD). After collection of the whole blood, it was allowed the blood to clot by leaving it undisturbed at room temperature for 30 minutes. The clot was removed by centrifuging at 1,000–2,000 x g for 10 minutes in a refrigerated centrifuge (4 C). The resulting supernatant is designated serum. The serum samples were aliquoted in 100 microliters and stored in a serum bank at -80C. These samples were collected in the Leprosy Outpatient Unit (Oswaldo Cruz Foundation, Rio de Janeiro, Brazil) and then they were sent in dry ice to Colorado State University, where it was processed and analyzed for metabolomics. At Colorado State University the samples were stored at -80C until processing. |
| Sample Type: | Blood |
| Storage Conditions: | -80C |
| Blood Serum Or Plasma: | serum |
Treatment:
| Treatment ID: | TR000930 |
| Treatment Summary: | No treatment of the patients was performed |
Sample Preparation:
| Sampleprep ID: | SP000923 |
| Sampleprep Summary: | The retrospective serum samples (80 microliters[ul]) were incubated with 3 volumes of cold methanol (100%) for 1 hour at -20C. After this incubation, the samples were centrifuged for 30 minutes at 18,000 xg at 4C to clear the supernatant. The supernatant was then transferred and dried under vacuum. Samples were re-suspended in 80 μl of 50% methanol. Prior to the injections on the LC-MS instrument, the samples were centrifuged for 30 minutes at 18,000 xg at 4oC. |
| Sampleprep Protocol ID: | SP000100 |
| Sampleprep Protocol Filename: | 060613_Methanol_Serum_Extraction |
| Sampleprep Protocol Comments: | Use always nitrile gloves. Do not use gloves with powder. Use pipette tips with aerosol barrier. |
| Processing Storage Conditions: | -80C |
| Extraction Method: | Methanol extraction |
| Extract Cleanup: | Centrifugation |
| Extract Storage: | -80C |
| Sample Resuspension: | 50% methanol |
| Sample Derivatization: | no derivatization process was performed |
Combined analysis:
| Analysis ID | AN001438 | AN001439 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 | Agilent 1290 |
| Column | Waters Xbridge BEH C18 XP (100 x 2.1mm,2.5um) | Waters Xbridge BEH C18 XP (100 x 2.1mm,2.5um) |
| MS Type | ESI | ESI |
| MS instrument type | TOF | TOF |
| MS instrument name | Agilent 6224 TOF | Agilent 6224 TOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH001009 |
| Chromatography Summary: | This was used for negative mode. The solvent gradient used for all chromatography was 2% solvent B for 3 min followed by a 15 min linear gradient of 2% to 98% solvent B, which was held for 0.3 min. Then returned to starting conditions over 1.2 min. Triplicate LC-MS injections were made of each sample and the order of sample injection (including triplicates) was randomized. |
| Instrument Name: | Agilent 1290 |
| Column Name: | Waters Xbridge BEH C18 XP (100 x 2.1mm,2.5um) |
| Column Temperature: | 50C |
| Flow Gradient: | 0.25 mL/min |
| Flow Rate: | 0.25 mL/min |
| Injection Temperature: | 4C |
| Sample Injection: | 20uL |
| Solvent A: | 89% water/5% acetonitrile/5% isopropanol; 5 mM ammonium acetate |
| Solvent B: | 50% acetonitrile/50% isopropanol; 5 mM ammonium acetate |
| Capillary Voltage: | 2.8 kV |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001010 |
| Chromatography Summary: | This was used for positive mode. The solvent gradient used for all chromatography was 2% solvent B for 3 min followed by a 15 min linear gradient of 2% to 98% solvent B, which was held for 0.3 min. Then returned to starting conditions over 1.2 min. Triplicate LC-MS injections were made of each sample and the order of sample injection (including triplicates) was randomized. |
| Instrument Name: | Agilent 1290 |
| Column Name: | Waters Xbridge BEH C18 XP (100 x 2.1mm,2.5um) |
| Column Temperature: | 50C |
| Flow Gradient: | 0.25 mL/min |
| Flow Rate: | 0.25 mL/min |
| Injection Temperature: | 4C |
| Sample Injection: | 20uL |
| Solvent A: | 95% water/5% acetonitrile; 0.1% formic acid |
| Solvent B: | 95% acetonitrile/5% water; 0.1% formic acid |
| Capillary Voltage: | 4.0kV |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001328 |
| Analysis ID: | AN001438 |
| Instrument Name: | Agilent 6224 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 2.8kV |
| Dry Gas Flow: | 5 L/min |
| Dry Gas Temp: | 310C |
| Fragment Voltage: | 120V |
| Nebulizer: | 20 psig |
| Scanning Range: | 2 spectra per second |
| Skimmer Voltage: | 50V |
| MS ID: | MS001329 |
| Analysis ID: | AN001439 |
| Instrument Name: | Agilent 6224 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 4.0kV |
| Dry Gas Flow: | 5 L/min |
| Dry Gas Temp: | 310C |
| Fragment Voltage: | 120V |
| Nebulizer: | 20 psig |
| Scanning Range: | 2 spectra per second |
| Skimmer Voltage: | 50V |
