Summary of Study ST001815

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 PR001148. The data can be accessed directly via it's Project DOI: 10.21228/M89Q5T This work is supported by NIH grant, U2C- DK119886.

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Study IDST001815
Study TitleMetabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis
Study TypeClinical
Study SummaryPlasma from children with juvenile idiopathic arthritis collected pre-treatment and following 3 months of treatment with methotrexate were submitted for metabolomic profiling to the NIH West Coast Metabolomics Center.
Institute
University of Kansas
DepartmentPharmacy Practice
LaboratoryFunk Lab
Last Namefunk
First Nameryan
Address2106 Olathe Boulevard
Emailryanfunk@kumc.edu
Phone9135885000
Submit Date2021-05-18
Num Groups1
Total Subjects30
Num Males9
Num Females21
Analysis Type DetailGC-MS/LC-MS
Release Date2021-06-17
Release Version1
ryan funk ryan funk
https://dx.doi.org/10.21228/M89Q5T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001148
Project DOI:doi: 10.21228/M89Q5T
Project Title:Metabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis
Project Type:Clinical
Project Summary:Association of changes in the plasma metabolome with clinical response to methotrexate in children with juvenile idiopathic arthritis.
Institute:University of Kansas
Department:Pharmacy Practice
Laboratory:Funk
Last Name:Funk
First Name:Ryan
Address:2106 Olathe Boulevard, Kansas City, Kansas, 66160, USA
Email:ryanfunk@kumc.edu
Phone:9139456904
Funding Source:KL2TR002367

Subject:

Subject ID:SU001892
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:1.8 to 17 years
Gender:Not applicable

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Subject Timepoint
SA16891410.010 -
SA16891510.310 3
SA16891611.011 -
SA16891711.311 3
SA16891812.012 -
SA16891912.312 3
SA16892014.014 -
SA16892114.314 3
SA16892220.020 -
SA16892320.320 3
SA16892422.022 -
SA16892522.322 3
SA16892624.024 -
SA16892724.324 3
SA16892825.025 -
SA16892925.325 3
SA16893029.029 -
SA16893129.329 3
SA1689322.02 -
SA1689332.32 3
SA16893430.030 -
SA16893530.330 3
SA16893635.035 -
SA16893735.335 3
SA16893836.036 -
SA16893936.336 3
SA16894037.037 -
SA16894137.337 3
SA16894238.038 -
SA16894338.338 3
SA16894440.040 -
SA16894540.340 3
SA16894645.045 -
SA16894745.345 3
SA16894849.049 -
SA16894949.349 3
SA16895050.050 -
SA16895150.350 3
SA16895251.051 -
SA16895351.351 3
SA16895458.058 -
SA16895558.358 3
SA16895659.059 -
SA16895759.359 3
SA16895860.060 -
SA16895960.360 3
SA16896061.061 -
SA16896161.361 3
SA16896262.062 -
SA16896362.362 3
SA16896463.063 -
SA16896564.064 -
SA16896663.664 3
SA16896764.364 3
SA16896866.066 -
SA16896966.366 3
SA1689708.08 -
SA1689718.38 3
SA1689729.09 -
SA1689739.39 3
Showing results 1 to 60 of 60

Collection:

Collection ID:CO001885
Collection Summary:Venous blood samples were collected in K2-EDTA containing tubes prior to initiation of MTX and at the patient’s routine 3 month follow up clinic visit along with routine laboratory blood draws. Venous blood samples (10 mL) collected at each timepoint were separated into plasma and cellular fractions by centrifugations at 2,000 RPM in a Beckman tabletop centrifuge for 10 minutes. The resulting supernatant (i.e. plasma fraction) was separated into aliquots and stored at -80 ºC prior to analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃
Additives:K2EDTA

Treatment:

Treatment ID:TR001905
Treatment Summary:Plasma samples were acquired from a single-center prospective cohort of JIA patients. The study included patients diagnosed with JIA requiring initiation of MTX for inadequately controlled disease without the need for biological therapy at initiation. Diagnosis of JIA was established based on the Edmonton 2001 International League of Associations of Rheumatology (ILAR) criteria for JIA. Patients were initiated on a standardized MTX dose of 15 mg/m2 weekly by subcutaneous or oral administration along with 1 mg folic acid daily. Concurrent medications allowed included nonsteroidal anti-inflammatory drugs (NSAIDs) and daily low-dose steroids (the lesser of 0.2 mg/kg/day or 10 mg). Intra-articular steroid injections (IASI) were allowed, however injected joints were counted as “active” at follow up to reduce the potential bias resulting from IASI.
Treatment Compound:Methotrexate
Treatment Route:Oral or Subcutaneous
Treatment Dose:15 mg/m^2
Treatment Doseduration:3 months

Sample Preparation:

Sampleprep ID:SP001898
Sampleprep Summary:Plasma samples were sent to the West Coast Metabolomics Center and were processed on laboratory Standard Operating Procedures for Sample Preparation of Blood Plasma or Serum Samples for Lipidomic, Biogenic Amine, and Primary Metabolomic Analysis using a biphasic MeOH/MTBE/Water extraction procedure. The upper organic phase was used for lipidomics analysis and the aqueous phase was used for analysis of primary metabolism and biogenic amines.

Combined analysis:

Analysis ID AN002944 AN002945 AN002946 AN002947
Analysis type MS MS MS MS
Chromatography type GC HILIC Reversed phase Reversed phase
Chromatography system Leco Pegasus IV GC Agilent 6530 Agilent 6530 Agilent 6530
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type EI ESI ESI ESI
MS instrument type GC-TOF QTOF QTOF QTOF
MS instrument name Leco Pegasus IV TOF Agilent 6530 QTOF Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode NEGATIVE POSITIVE POSITIVE NEGATIVE
Units Peak Height Intensity Peak Height Intensity Peak Height Intensity Peak Height Intensity

Chromatography:

Chromatography ID:CH002180
Chromatography Summary:Primary Metabolism
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC
  
Chromatography ID:CH002181
Chromatography Summary:Biogenic Amines
Instrument Name:Agilent 6530
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC
  
Chromatography ID:CH002182
Chromatography Summary:Lipidomics
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:65
Flow Rate:0.6 mL/min
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS002734
Analysis ID:AN002944
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:NEGATIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
  
MS ID:MS002735
Analysis ID:AN002945
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:POSITIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf
  
MS ID:MS002736
Analysis ID:AN002946
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:POSITIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
  
MS ID:MS002737
Analysis ID:AN002947
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols.
Ion Mode:NEGATIVE
Analysis Protocol File:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
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