Summary of study ST001121

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.


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Study IDST001121
Study TitleIdentification of urine metabolites in patients with interstitial cystitis using untargeted metabolomics (part I)
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 charged surface hybrid (CSH) 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
Analysis Type DetailLC-MS
Release Date2019-02-26
Release Version1
Ivana Blaženović Ivana Blaženović application/zip

Select appropriate tab below to view additional metadata details:


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:SU001182
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
SA077842IC29_50Interstitial cystitis
SA077843IC30_51Interstitial cystitis
SA077844IC32_53Interstitial cystitis
SA077845IC28_49Interstitial cystitis
SA077846IC31_52Interstitial cystitis
SA077847IC27_48Interstitial cystitis
SA077848IC24_45Interstitial cystitis
SA077849IC25_46Interstitial cystitis
SA077850IC26_47Interstitial cystitis
SA077851IC33_54Interstitial cystitis
SA077852IC35_56Interstitial cystitis
SA077853IC40_61Interstitial cystitis
SA077854IC41_62Interstitial cystitis
SA077855IC42_63Interstitial cystitis
SA077856IC43_64Interstitial cystitis
SA077857IC39_60Interstitial cystitis
SA077858IC38_59Interstitial cystitis
SA077859IC23_44Interstitial cystitis
SA077860IC36_57Interstitial cystitis
SA077861IC37_58Interstitial cystitis
SA077862IC34_55Interstitial cystitis
SA077863IC22_43Interstitial cystitis
SA077864IC7_28Interstitial cystitis
SA077865IC8_29Interstitial cystitis
SA077866IC9_30Interstitial cystitis
SA077867IC10_31Interstitial cystitis
SA077868IC6_27Interstitial cystitis
SA077869IC5_26Interstitial cystitis
SA077870IC2_23Interstitial cystitis
SA077871IC3_24Interstitial cystitis
SA077872IC4_25Interstitial cystitis
SA077873IC11_32Interstitial cystitis
SA077874IC12_33Interstitial cystitis
SA077875IC18_39Interstitial cystitis
SA077876IC19_40Interstitial cystitis
SA077877IC20_41Interstitial cystitis
SA077878IC21_42Interstitial cystitis
SA077879IC17_38Interstitial cystitis
SA077880IC16_37Interstitial cystitis
SA077881IC13_34Interstitial cystitis
SA077882IC14_35Interstitial cystitis
SA077883IC15_36Interstitial cystitis
SA077884IC1_22Interstitial cystitis
Showing results 1 to 43 of 43


Collection ID:CO001176
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:TR001197
Treatment Summary:Patients were not receiving any treatment at the time the urine was collected.

Sample Preparation:

Sampleprep ID:SP001190
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 lipidomics analysis, samples were resuspened in 110 µL of 9:1 methanol:toluene with 50 nM of CUDA 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. 100 µL of the supernatant was removed and submited to lipidomics analysis.

Combined analysis:

Analysis ID AN001846
Analysis type MS
Chromatography type CSH
Chromatography system Thermo Vanquish
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Units Peak Height


Chromatography ID:CH001323
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:600 bar - 900 bar
Column Temperature:65°C
Flow Gradient:0 min 15% B; 0−2 min 30% B; 2−2.5 min 48% B; 2.5−11 min 82% B; 11−11.5 min 99% B; 11.5−12 min 99% B; 12−12.1 min 15% B; 12.1−15 min 15% B.
Flow Rate:600 µL/min
Internal Standard:50 nM CUDA
Sample Injection:1 µL
Solvent A:acetonitrile:water (60:40, v/v) with ammonium formate (10 mM) and formic acid (0.1%)
Solvent B:2-propanol:acetonitrile (90:10, v/v) with ammonium formate (10 mM) and formic acid (0.1%).
Chromatography Type:CSH


MS ID:MS001707
Analysis ID:AN001846
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.