Summary of Study ST003520
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 PR002165. The data can be accessed directly via it's Project DOI: 10.21228/M8S247 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003520 |
| Study Title | Identification of Plasma Metabolomic Biomarkers of Juvenile Idiopathic Arthritis |
| Study Type | Clinical |
| Study Summary | This study utilizes plasma metabolomic profiling to identify biomarkers associated with juvenile idiopathic arthritis (JIA) by analyzing samples from treatment-naïve JIA patients and non-JIA controls. Significant metabolic alterations were detected, with sphingosine metabolites and fatty acid ethanolamides showing notable increases in JIA patients, while specific compounds such as sarcosine were decreased. The research highlights 11 highly discriminatory metabolites, including sphinganine-1-phosphate, demonstrating potential for improved JIA diagnosis and treatment through targeted metabolic profiling. |
| Institute | University of Kansas |
| Department | Center for Computational Biology |
| Laboratory | Funk |
| Last Name | Kumar |
| First Name | Amar |
| Address | Multidisciplinary Research Bldg. 2030 Becker Drive Lawrence, KS 66047 |
| amarkumar@ku.edu | |
| Phone | 18723016225 |
| Submit Date | 2024-09-09 |
| Num Groups | 2 |
| Total Subjects | 210 |
| Num Males | 82 |
| Num Females | 128 |
| Study Comments | Although the raw dataset initially included 210 subjects, only 207 were included in the final analysis due to consent-related exclusions. These three subjects were removed to ensure compliance with ethical standards. |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005778 | AN005779 | AN005780 | AN005781 |
|---|---|---|---|---|
| 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 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 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 | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH004385 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Solvent B: | 100% methanol; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004386 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes. |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Solvent B: | 50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004387 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 6.5 mM ammonium bicarbonate, pH 8 |
| Solvent B: | 95% methanol/5% water; 6.5 mM ammonium bicarbonate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004388 |
| Chromatography Summary: | HILIC (LC/MS Polar Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with ammonium hydroxide) |
| Solvent B: | 50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with ammonium hydroxide) |
| Chromatography Type: | HILIC |
