Summary of Study ST000882
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000611. The data can be accessed directly via it's Project DOI: 10.21228/M8XQ41 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST000882 |
| Study Title | Untargeted metabolomics data of leprosy patients with type 1 reaction |
| Study Type | Untargeted MS qualitative analysis in retrospective serum samples of leprosy patients with type 1 reaction |
| Study Summary | Untargeted metabolomics-based analyses of sera from 7 patients with and 9 without T1R were conducted via liquid chromatography–mass spectrometry. |
| Institute | Colorado State University |
| Department | Department of Microbiology, Immunology, and Pathology |
| Laboratory | Belisle |
| Last Name | Silva |
| First Name | Carlos |
| Address | Rampart Road, 1682 Campus Delivery |
| cadriano@rams.colostate.edu | |
| Phone | 9702154962 |
| Submit Date | 2017-06-19 |
| Num Groups | 2 |
| Total Subjects | 16 |
| Num Males | 5 |
| Num Females | 11 |
| Study Comments | 2 groups (first group was leprosy patients with type 1 reaction, N=9; and second group was leprosy patients without type 1 reaction, N=7) 5 males (3 were leprosy patients with type 1 reaction and 2 were leprosy patients without type 1 reaction), 11 females (4 were leprosy patients with type 1 reaction and 7 were leprosy patients without type 1 reaction). For this study we used retrospective sera samples. |
| Publications | J Infect Dis. 2017 Feb 1;215(3):431-439. doi: 10.1093/infdis/jiw541. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-06-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000611 |
| Project DOI: | doi: 10.21228/M8XQ41 |
| Project Title: | Metabolomics analysis of leprosy patients with type 1 reaction |
| Project Type: | MS qualitative analysis and identification of polyunsaturated fatty acids in retrospective serum samples of leprosy patients with type 1 reaction |
| Project Summary: | Type 1 reaction (T1R) is an acute inflammatory episode that causes severe neuronal damages in patients with leprosy. The factors that trigger this pathology is still unknown, and further studies are needed to understand T1R and to early prevent its start. It is well established that the host immune response is linked to T1R and previous studies indicated that the metabolism of the host also influences the adaptive immune response against M. leprae antigens. Therefore, metabolomics-based analyses of sera from 7 patients with and 9 without T1R were conducted via liquid chromatography–mass spectrometry. The main goal of this project was to determine whether the metabolism of polyunsaturated fatty acids (such as eicosanoids and omega-3 fatty acids) were perturbed in leprosy patients with T1R. |
| Institute: | Colorado State University |
| Department: | Department of Microbiology, Immunology, and Pathology |
| Laboratory: | Belisle |
| Last Name: | Belisle |
| First Name: | John |
| Address: | Rampart Road, 1682 Campus Delivery |
| Email: | cadriano@rams.colostate.edu |
| Phone: | 9704819160 |
| Funding Source: | This work was supported by the New York Community Trust (grant to J. T. B. as co–principle investigator [PI]), by the Heiser Foundation (grant to J. T. B. as co-PI), and by the Brazilian Coordination for the Improvement of Higher Education Personnel through the Science without Borders program (10546-13-8, for the postdoctoral scholarship to C. A. M. S.). |
| Project Comments: | The institutional review boards of Colorado State University approved the use of sera for the reported study. |
| Publications: | J Infect Dis. 2017 Feb 1;215(3):431-439. doi: 10.1093/infdis/jiw541. |
| Contributors: | Carlos A. M. Silva, Kristofor Webb, Barbara G. Andre, Maria Angela Marques, Fernanda Marques Carvalho, Cristiana Santos de Macedo, Roberta Olmo Pinheiro, Euzenir Nunes Sarno, Maria Cristina Vidal Pessolani, John T. Belisle. |
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:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Type 1 reaction (T1R) |
|---|---|---|
| SA051152 | S15 | No |
| SA051153 | S14 | No |
| SA051154 | S16 | No |
| SA051155 | S18 | No |
| SA051156 | S19 | No |
| SA051157 | S13 | No |
| SA051158 | S17 | No |
| SA051159 | S12 | No |
| SA051160 | S11 | No |
| SA051161 | S5 | Yes |
| SA051162 | S3 | Yes |
| SA051163 | S7 | Yes |
| SA051164 | S9 | Yes |
| SA051165 | S10 | Yes |
| SA051166 | S1 | Yes |
| SA051167 | S8 | Yes |
| Showing results 1 to 16 of 16 |
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 |
