Summary of Study ST000382

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 PR000299. The data can be accessed directly via it's Project DOI: 10.21228/M8D60P This work is supported by NIH grant, U2C- DK119886.

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Study IDST000382
Study TitleUrinary Metabolites in IC/PBS Diagnosis (part II)
Study TypeDisease
Study SummaryThis West Coast Metabolomics Center sponsored pilot grant goal is to identify and validate interstitial cystitis/painful bladder syndrome (IC/PBS)-associated urinary metabolites. Our central hypothesis is that IC/PBS-associated metabolites in the urine of IC/PBS patients can segregate patients from control subjects, and that their levels are correlated with clinical symptoms. To test this hypothesis, we will identify IC/PBS-associated metabolites in urine using two independent platforms, GC-MS and quadrupole time-of-flight (Q-TOF) mass spectrometry under the collaboration with UC Davis WCMC scientists. We believe that this study will provide a significant potential clinical impact because results may lead to clinical methods to increase diagnostic accuracy and an improved understanding of the molecular basis of IC/PBS and its relationship to urologic conditions with overlapping symptoms.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
AddressHealth Sciences Drive, Davis, California, 95616, USA
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-04-25
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8D60P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000299
Project DOI:doi: 10.21228/M8D60P
Project Title:Urinary Metabolites in IC/PBS Diagnosis
Project Summary:This West Coast Metabolomics Center sponsored pilot grant goal is to identify and validate interstitial cystitis/painful bladder syndrome (IC/PBS)-associated urinary metabolites. Our central hypothesis is that IC/PBS-associated metabolites in the urine of IC/PBS patients can segregate patients from control subjects, and that their levels are correlated with clinical symptoms. To test this hypothesis, we will identify IC/PBS-associated metabolites in urine using two independent platforms, GC-MS and quadrupole time-of-flight (Q-TOF) mass spectrometry under the collaboration with UC Davis WCMC scientists. We believe that this study will provide a significant potential clinical impact because results may lead to clinical methods to increase diagnostic accuracy and an improved understanding of the molecular basis of IC/PBS and its relationship to urologic conditions with overlapping symptoms.
Institute:University of California, Davis
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154

Subject:

Subject ID:SU000403
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Cohort Treatment SubCondition
SA017325Inj029_SA090_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017326Inj080_SA092_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017327Inj031_SA089_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017328Inj087_SA087_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017329Inj024_SA086_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017330Inj067_SA093_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017331Inj075_SA088_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017332Inj093_SA091_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017333Inj042_SA098_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017334Inj001_SA099_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017335Inj040_SA094_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017336Inj050_SA097_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017337Inj043_SA100_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017338Inj008_SA096_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017339Inj041_SA095_KimUrine.dCSMC IC/PBS Urine SEVERE
SA017340Inj047_SA075_KimUrine.dCSMC Matched Control Urine n/a
SA017341Inj059_SA077_KimUrine.dCSMC Matched Control Urine n/a
SA017342Inj072_SA076_KimUrine.dCSMC Matched Control Urine n/a
SA017343Inj081_SA074_KimUrine.dCSMC Matched Control Urine n/a
SA017344Inj002_SA072_KimUrine.dCSMC Matched Control Urine n/a
SA017345Inj023_SA078_KimUrine.dCSMC Matched Control Urine n/a
SA017346Inj039_SA071_KimUrine.dCSMC Matched Control Urine n/a
SA017347Inj074_SA073_KimUrine.dCSMC Matched Control Urine n/a
SA017348Inj015_SA084_KimUrine.dCSMC Matched Control Urine n/a
SA017349Inj044_SA079_KimUrine.dCSMC Matched Control Urine n/a
SA017350Inj026_SA085_KimUrine.dCSMC Matched Control Urine n/a
SA017351Inj062_SA082_KimUrine.dCSMC Matched Control Urine n/a
SA017352Inj005_SA083_KimUrine.dCSMC Matched Control Urine n/a
SA017353Inj073_SA081_KimUrine.dCSMC Matched Control Urine n/a
SA017354Inj091_SA080_KimUrine.dCSMC Matched Control Urine n/a
SA017355Inj032_SA065_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017356Inj088_SA057_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017357Inj063_SA067_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017358Inj003_SA049_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017359Inj070_SA070_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017360Inj017_SA069_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017361Inj035_SA054_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017362Inj085_SA035_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017363Inj055_SA031_KimUrine.dINHA IC/PBS Urine INTERMEDIATE
SA017364Inj037_SA068_KimUrine.dINHA IC/PBS Urine MODEST
SA017365Inj033_SA040_KimUrine.dINHA IC/PBS Urine MODEST
SA017366Inj045_SA064_KimUrine.dINHA IC/PBS Urine MODEST
SA017367Inj082_SA060_KimUrine.dINHA IC/PBS Urine MODEST
SA017368Inj038_SA039_KimUrine.dINHA IC/PBS Urine MODEST
SA017369Inj027_SA045_KimUrine.dINHA IC/PBS Urine MODEST
SA017370Inj058_SA032_KimUrine.dINHA IC/PBS Urine MODEST
SA017371Inj086_SA034_KimUrine.dINHA IC/PBS Urine MODEST
SA017372Inj018_SA059_KimUrine.dINHA IC/PBS Urine MODEST
SA017373Inj061_SA038_KimUrine.dINHA IC/PBS Urine MODEST
SA017374Inj092_SA036_KimUrine.dINHA IC/PBS Urine MODEST
SA017375Inj079_SA044_KimUrine.dINHA IC/PBS Urine MODEST
SA017376Inj065_SA053_KimUrine.dINHA IC/PBS Urine MODEST
SA017377Inj016_SA052_KimUrine.dINHA IC/PBS Urine MODEST
SA017378Inj071_SA051_KimUrine.dINHA IC/PBS Urine MODEST
SA017379Inj054_SA048_KimUrine.dINHA IC/PBS Urine MODEST
SA017380Inj013_SA055_KimUrine.dINHA IC/PBS Urine MODEST
SA017381Inj083_SA058_KimUrine.dINHA IC/PBS Urine SEVERE
SA017382Inj094_SA029_KimUrine.dINHA IC/PBS Urine SEVERE
SA017383Inj084_SA028_KimUrine.dINHA IC/PBS Urine SEVERE
SA017384Inj060_SA050_KimUrine.dINHA IC/PBS Urine SEVERE
SA017385Inj014_SA046_KimUrine.dINHA IC/PBS Urine SEVERE
SA017386Inj053_SA033_KimUrine.dINHA IC/PBS Urine SEVERE
SA017387Inj048_SA047_KimUrine.dINHA IC/PBS Urine SEVERE
SA017388Inj012_SA037_KimUrine.dINHA IC/PBS Urine SEVERE
SA017389Inj052_SA030_KimUrine.dINHA IC/PBS Urine SEVERE
SA017390Inj025_SA062_KimUrine.dINHA IC/PBS Urine SEVERE
SA017391Inj089_SA061_KimUrine.dINHA IC/PBS Urine SEVERE
SA017392Inj030_SA056_KimUrine.dINHA IC/PBS Urine SEVERE
SA017393Inj078_SA063_KimUrine.dINHA IC/PBS Urine SEVERE
SA017394Inj022_SA043_KimUrine.dINHA IC/PBS Urine SEVERE
SA017395Inj010_SA042_KimUrine.dINHA IC/PBS Urine SEVERE
SA017396Inj019_SA041_KimUrine.dINHA IC/PBS Urine SEVERE
SA017397Inj064_SA066_KimUrine.dINHA IC/PBS Urine SEVERE
SA017398Inj007_SA013_KimUrine.dINHA Matched Control Urine n/a
SA017399Inj049_SA014_KimUrine.dINHA Matched Control Urine n/a
SA017400Inj034_SA016_KimUrine.dINHA Matched Control Urine n/a
SA017401Inj004_SA012_KimUrine.dINHA Matched Control Urine n/a
SA017402Inj090_SA015_KimUrine.dINHA Matched Control Urine n/a
SA017403Inj006_SA010_KimUrine.dINHA Matched Control Urine n/a
SA017404Inj077_SA017_KimUrine.dINHA Matched Control Urine n/a
SA017405Inj057_SA008_KimUrine.dINHA Matched Control Urine n/a
SA017406Inj009_SA009_KimUrine.dINHA Matched Control Urine n/a
SA017407Inj068_SA011_KimUrine.dINHA Matched Control Urine n/a
SA017408Inj021_SA022_KimUrine.dINHA Matched Control Urine n/a
SA017409Inj046_SA024_KimUrine.dINHA Matched Control Urine n/a
SA017410Inj028_SA025_KimUrine.dINHA Matched Control Urine n/a
SA017411Inj069_SA026_KimUrine.dINHA Matched Control Urine n/a
SA017412Inj011_SA027_KimUrine.dINHA Matched Control Urine n/a
SA017413Inj036_SA023_KimUrine.dINHA Matched Control Urine n/a
SA017414Inj076_SA007_KimUrine.dINHA Matched Control Urine n/a
SA017415Inj051_SA019_KimUrine.dINHA Matched Control Urine n/a
SA017416Inj066_SA020_KimUrine.dINHA Matched Control Urine n/a
SA017417Inj056_SA021_KimUrine.dINHA Matched Control Urine n/a
SA017418Inj020_SA018_KimUrine.dINHA Matched Control Urine n/a
Showing results 1 to 94 of 94

Collection:

Collection ID:CO000397
Collection Summary:All urine specimens were collected in the morning by clean catch methods. Samples were centrifuged at 4◦C to remove cell debris, and supernatants were aliquots of 1ml/tube, before storage at −80◦C until further analysis.
Sample Type:Urine

Treatment:

Treatment ID:TR000417
Treatment Summary:Matched control urine vs. IC/PBS Urine

Sample Preparation:

Sampleprep ID:SP000410
Sampleprep Summary:1. The dry sample is resuspended in 50 uL of Water/acetonitrile 95:5 containing 100 ng/mL of CUDA (12-[[(cyclohexylamino)carbonyl]amino]-dodecanoic acid) as internal standard, vortexed for 10 sec, sonicated for 5 minutes, then centrifuged for 3 min at 14,000 rcf. 2. The samples are transferred to amber vials with micro-inserts and capped immediately, and stored at 4 degree C until and during analysis
Sampleprep Protocol Filename:SP_RP18_Protocol_KimUrine_IG102814.docx

Combined analysis:

Analysis ID AN000616 AN000617
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity BEH C18 (100 x 2.1mm,1.7um) Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode POSITIVE NEGATIVE
Units counts counts

Chromatography:

Chromatography ID:CH000442
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
Column Pressure:1200 bar
Column Temperature:65 C
Flow Gradient:0% B to 99%B
Flow Rate:0.5 mL/min
Internal Standard:CUDA
Sample Injection:3uL
Solvent A:95% water/5% acetonitrile; 0.1% acetic acid
Solvent B:100% acetonitrile; 0.1% acetic acid
Analytical Time:15 min
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel generated
Chromatography Type:Reversed phase

MS:

MS ID:MS000549
Analysis ID:AN000616
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 L/min
Dry Gas Temp:325 C
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325 C
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 L/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:extended dynamic range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000550
Analysis ID:AN000617
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 L/min
Dry Gas Temp:200 C
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325 C
Ion Spray Voltage:1000
Ionization:Neg
Dataformat:.d
Desolvation Gas Flow:11 L/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2Hz
Scanning Range:60-1700
Skimmer Voltage:65
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