Summary of Study ST001122

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000752. The data can be accessed directly via it's Project DOI: 10.21228/M8GD6N This work is supported by NIH grant, U2C- DK119886.


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.

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Study IDST001122
Study TitleIdentification of urine metabolites in patients with interstitial cystitis using untargeted metabolomics (part II)
Study SummaryUrine metabolites are used in many clinical and biomedical studies, but usually only for a few classic compounds. Metabolomics detects vastly more metabolic signals that may be used to precisely define the health status of individuals. However, many compounds remain unidentified, hampering biochemical conclusions. Here, we annotate all metabolites detected using an untargeted metabolomics approach with a hydrophilic interaction liquid chromatography (HILIC) assay on a Q Exactive HF mass spectrometry.
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameBlaženović
First NameIvana
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Phone(530) 754-8258
Submit Date2019-01-15
Total Subjects43
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-02-26
Release Version1
Ivana Blaženović Ivana Blaženović application/zip

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Project ID:PR000752
Project DOI:doi: 10.21228/M8GD6N
Project Title:Lipidomic analysis of urine in patients with interstitial cystitis.
Project Summary:The urine of 43 patients with interstitial cystitis was analyzed using the WCMC lipidomics method. The target goal of this project is to identify urinary metabolites in patients with urological disorders.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Phone:(530) 754-8258


Subject ID:SU001183
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606


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

mb_sample_id local_sample_id Condition
SA077885IC29_50Interstitial cystitis
SA077886IC30_51Interstitial cystitis
SA077887IC32_53Interstitial cystitis
SA077888IC28_49Interstitial cystitis
SA077889IC31_52Interstitial cystitis
SA077890IC27_48Interstitial cystitis
SA077891IC24_45Interstitial cystitis
SA077892IC25_46Interstitial cystitis
SA077893IC26_47Interstitial cystitis
SA077894IC33_54Interstitial cystitis
SA077895IC35_56Interstitial cystitis
SA077896IC40_61Interstitial cystitis
SA077897IC41_62Interstitial cystitis
SA077898IC42_63Interstitial cystitis
SA077899IC43_64Interstitial cystitis
SA077900IC39_60Interstitial cystitis
SA077901IC38_59Interstitial cystitis
SA077902IC23_44Interstitial cystitis
SA077903IC36_57Interstitial cystitis
SA077904IC37_58Interstitial cystitis
SA077905IC34_55Interstitial cystitis
SA077906IC22_43Interstitial cystitis
SA077907IC7_28Interstitial cystitis
SA077908IC8_29Interstitial cystitis
SA077909IC9_30Interstitial cystitis
SA077910IC10_31Interstitial cystitis
SA077911IC6_27Interstitial cystitis
SA077912IC5_26Interstitial cystitis
SA077913IC2_23Interstitial cystitis
SA077914IC3_24Interstitial cystitis
SA077915IC4_25Interstitial cystitis
SA077916IC11_32Interstitial cystitis
SA077917IC12_33Interstitial cystitis
SA077918IC18_39Interstitial cystitis
SA077919IC19_40Interstitial cystitis
SA077920IC20_41Interstitial cystitis
SA077921IC21_42Interstitial cystitis
SA077922IC17_38Interstitial cystitis
SA077923IC16_37Interstitial cystitis
SA077924IC13_34Interstitial cystitis
SA077925IC14_35Interstitial cystitis
SA077926IC15_36Interstitial cystitis
SA077927IC1_22Interstitial cystitis
Showing results 1 to 43 of 43


Collection ID:CO001177
Collection Summary:Urine samples were collected from 43 patients with interstial cystitis. Urine was frozen to -80°C and shipped to the WCMC on dry ice, where samples were stored at -80°C until analysis.
Sample Type:Urine
Storage Conditions:-80℃


Treatment ID:TR001198
Treatment Summary:Patients were not receiving any treatment at the time the urine was collected.

Sample Preparation:

Sampleprep ID:SP001191
Sampleprep Summary:Samples were removed from the -80°C freezer and allowed to thaw on ice. 225 µL of MeOH with lipid internal standards was added to each sample. Samples were vortexed for 10 seconds. 750 µL of MTBE plus quality controls was added to each sample. Samples were vortexed for 10 seconds. 188 µL of LC-MS grade water was added to each sample. Samples were shaken at 4°C on an orbital mixing plate for 6 minutes. Samples were centrifuged for 2 minutes at 14,000 rcf. 2 aliquots of 350 µL were removed from the top, organic phase. One aliquot was stored at -20°C for backup and the other was dried using a Labconco centrivap. 2 aliquots of 125 µL of the bottom polar phase were removed. One aliquot was stored at -20°C for backup and the other was dried using a Labconco centrivap.
Sample Resuspension:For HILIC analysis, samples were resuspened in 100 µL of 9:1 methanol:toluene with deuterated compounds as an internal standard. Samples were vortexed for 10 seconds and then sonicated in room temperature water for 5 minutes. Samples were run in a centrifuge for 2 minutes at 16,100 rcf. 90 µL of the supernatant was removed and submitted to HILIC analysis.

Combined analysis:

Analysis ID AN001847
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Units Peak Height


Chromatography ID:CH001324
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:200 bar - 600 bar
Column Temperature:45°C
Flow Gradient:0 min 100% B; 0−2 min 100% B; 2−7.7 min 70% B; 7.7−9.5 min 40% B; 9.5−10.25 min 30% B; 10.25−12.75 min 100% B; 12.75−17 min 100% B
Flow Rate:400 µL/min
Sample Injection:1 µL
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC


MS ID:MS001708
Analysis ID:AN001847
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Comments:Data was processing using X-Calibur Qual Browser, MS-Dial, and MS-Flo following the data processing procedure outlined by the WCMC.