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 |
MS:
| MS ID: | MS005498 |
| Analysis ID: | AN005778 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005499 |
| Analysis ID: | AN005779 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005500 |
| Analysis ID: | AN005780 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005501 |
| Analysis ID: | AN005781 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar) - MS/MS was performed on a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Note: In our dataset, cells marked as 'blank (i.e. empty cells)' indicate that the metabolite was either not present in the sample or the measurement fell below the detection limits of our instruments. Essentially, we didn't find any trace of the metabolite, or it was too low to measure accurately. On the other hand, cells labeled 'ND' (which stands for "Not Detected") occur when we consolidate data from different experiments. If a metabolite wasn’t detected in one or more of the individual experiments but was present in others, we mark it as 'ND' in the consolidated dataset. This label helps us understand that while the metabolite was identified in some datasets, it was absent in others, possibly due to variations in experimental conditions or sample differences. By using these distinct labels, we ensure that anyone analyzing the data can clearly understand whether a metabolite was consistently undetectable across all experiments ('blank') or if it was found in some but not all ('ND'). This clarity helps in analyzing the data accurately, avoiding confusion between experimental absence and measurement limitations. |
| Ion Mode: | NEGATIVE |
