Summary of Study ST001682

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 PR001081. The data can be accessed directly via it's Project DOI: 10.21228/M8ZT4C This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST001682
Study TitleUntargeted urine LC-HRMS metabolomics profiling for bladder cancer binary outcome classification
Study SummaryTwo samples cohorts were analysed for bladder cancer biomarkers selection. Untargeted urine RP UPLC-HRMS metabolomics profiling was utilized in SCAN MS mode and positive polarity. Dilute and shoot technique was employed for sample preparation.
Institute
Lomonosov MSU
DepartmentChemistry
LaboratoryMass spectrometry
Last NamePlyushchenko
First NameIvan
AddressLeninskie gory, 1/3
Emailplyush1993@bk.ru
Phone+79160362200
Submit Date2020-10-20
Num Groups2
Total Subjects124
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailLC-MS
Release Date2021-02-22
Release Version1
Ivan Plyushchenko Ivan Plyushchenko
https://dx.doi.org/10.21228/M8ZT4C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001081
Project DOI:doi: 10.21228/M8ZT4C
Project Title:Untargeted urine LC-HRMS metabolomics profiling for bladder cancer binary outcome classification
Project Summary:Two samples cohorts were analysed for bladder cancer biomarkers selection. Untargeted urine RP UPLC-HRMS metabolomics profiling was utilized in SCAN MS mode and positive polarity. Dilute and shoot technique was employed for sample preparation.
Institute:Lomonosov Moscow State University
Department:Chemistry
Laboratory:Mass spectrometry
Last Name:Plyushchenko
First Name:Ivan
Address:Leninskie gory, 1/3
Email:plyush1993@bk.ru
Phone:+79160362200
Funding Source:Russian Foundation for Basic Research (RFBR)
Project Comments:research project No. 19-33-90071
Publications:Ivan V. Plyushchenko, et al. "Omics Untargeted Key Script: R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study" Journal of Proteome Research 2022 21 (3), 833-847. DOI: 10.1021/acs.jproteome.1c00392
Contributors:Rodin Igor, Glukhov Alexander

Subject:

Subject ID:SU001759
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:19-87
Gender:Male and female
Human Race:Caucasian

Factors:

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

mb_sample_id local_sample_id Label Batch
SA154813s9_2CG b1
SA154814s6_1CG b1
SA154815s4_1CG b1
SA154816s4_2CG b1
SA154817s9_1CG b1
SA154818s6_2CG b1
SA154819s95_2CG b10
SA154820s96_2CG b10
SA154821s91_1CG b10
SA154822s94_2CG b10
SA154823s91_2CG b10
SA154824s93_1CG b10
SA154825s94_1CG b10
SA154826s95_1CG b10
SA154827s96_1CG b10
SA154828s93_2CG b10
SA154829s105_1CG b11
SA154830s105_2CG b11
SA154831s109_1CG b11
SA154832s109_2CG b11
SA154833s117_2CG b12
SA154834s120_2CG b12
SA154835s112_2CG b12
SA154836s116_2CG b12
SA154837s112_1CG b12
SA154838s120_1CG b12
SA154839s116_1CG b12
SA154840s117_1CG b12
SA154841s124_1CG b13
SA154842s124_2CG b13
SA154843s11_2CG b2
SA154844s14_2CG b2
SA154845s20_2CG b2
SA154846s18_2CG b2
SA154847s19_2CG b2
SA154848s13_2CG b2
SA154849s11_1CG b2
SA154850s13_1CG b2
SA154851s14_1CG b2
SA154852s18_1CG b2
SA154853s20_1CG b2
SA154854s19_1CG b2
SA154855s25_1CG b3
SA154856s29_1CG b3
SA154857s23_2CG b3
SA154858s29_2CG b3
SA154859s27_2CG b3
SA154860s25_2CG b3
SA154861s23_1CG b3
SA154862s21_2CG b3
SA154863s27_1CG b3
SA154864s21_1CG b3
SA154865s36_2CG b4
SA154866s33_2CG b4
SA154867s37_2CG b4
SA154868s36_1CG b4
SA154869s33_1CG b4
SA154870s37_1CG b4
SA154871s48_2CG b5
SA154872s46_1CG b5
SA154873s50_2CG b5
SA154874s41_2CG b5
SA154875s50_1CG b5
SA154876s48_1CG b5
SA154877s41_1CG b5
SA154878s45_2CG b5
SA154879s45_1CG b5
SA154880s42_1CG b5
SA154881s46_2CG b5
SA154882s42_2CG b5
SA154883s52_1CG b6
SA154884s51_1CG b6
SA154885s51_2CG b6
SA154886s59_2CG b6
SA154887s60_2CG b6
SA154888s55_2CG b6
SA154889s52_2CG b6
SA154890s59_1CG b6
SA154891s60_1CG b6
SA154892s55_1CG b6
SA154893s63_2CG b7
SA154894s65_2CG b7
SA154895s67_2CG b7
SA154896s69_2CG b7
SA154897s70_2CG b7
SA154898s61_2CG b7
SA154899s70_1CG b7
SA154900s63_1CG b7
SA154901s67_1CG b7
SA154902s69_1CG b7
SA154903s61_1CG b7
SA154904s65_1CG b7
SA154905s74_2CG b8
SA154906s73_2CG b8
SA154907s77_2CG b8
SA154908s78_2CG b8
SA154909s71_1CG b8
SA154910s79_2CG b8
SA154911s71_2CG b8
SA154912s80_1CG b8
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Collection:

Collection ID:CO001752
Collection Summary:All morning fasting urine samples were collected in sterilized plastic sealed falcons for this study and were frozen in the refrigerator at -80 °C. All the samples were defrosted at room temperature prior the analysis. The quality control (QC) sample was prepared from a mix of all urine samples that were participated in this research in equal volume, then were filled into separate containers and were stored together with other samples. A new aliquot (from individual container) of QC was used in each new day of analysis.
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001772
Treatment Summary:Creatinine level, age, sex and clinical diagnosis were collected for study samples as meta-data. The study included urine samples from patients with bladder cancer (TG) and healthy controls (CG) matched with the TG group for age and sex.

Sample Preparation:

Sampleprep ID:SP001765
Sampleprep Summary:Briefly, dilute and shoot technique was utilized. Prior to analysis, samples were defrosted at room temperature and vortexed vigorously and centrifuged at 16000 rpm for 15 min, then aliquots of the supernatant were diluted in 5-fold by deionized water with a final papaverine concentration of 0.2 µg mL-1 (IS), vortexed vigorously and centrifuged at 16000 rpm for 15 min and then aliquots of supernatant were placed into vials.
Processing Storage Conditions:Room temperature
Extract Storage:Room temperature

Combined analysis:

Analysis ID AN002746
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI
MS instrument type Other
MS instrument name Shimadzu LCMS-IT-TOF
Ion Mode POSITIVE
Units area

Chromatography:

Chromatography ID:CH002028
Chromatography Summary:The apparatus consisted of a two LC-20AD pumps (Shimadzu, Japan), an automatic sample injector, coupled on-line with an LCMS-IT-TOF (Shimadzu, Japan) mass spectrometer with an electrospray ionization source. The HPLC separation was conducted on a 2.1 × 100 mm Waters Acquity UPLC BEH; 1.7 μm column (Waters, Milford MA, USA) with 2.1 × 5 mm UHPLC Guard 3PK Zorbax SB-C18 1.8 μm guard column (Agilent Technologies, USA). Two solvents were used: (A) deionized water with 0,1% formic acid, and (B) MeCN. After a 5 min hold at 5% solvent B, elution was performed according to the following conditions: from 5% B to 40% B in 20 min; to 95% B in 7 min; keeping constant for 10 min, to 5% B in 3 min, followed by 5 min of equilibration on the initial conditions. Total analysis time was 50 min. Column temperature was 35˚C. Autosampler tray temperature was 4˚C.
Instrument Name:Shimadzu 20AD
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Pressure:300-500 bar
Column Temperature:35
Flow Gradient:non-linear
Flow Rate:0.3 ml/min
Injection Temperature:5
Internal Standard:papaverine
Sample Injection:5 mkl
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Analytical Time:50 min
Chromatography Type:Reversed phase

MS:

MS ID:MS002543
Analysis ID:AN002746
Instrument Name:Shimadzu LCMS-IT-TOF
Instrument Type:Other
MS Type:ESI
MS Comments:The apparatus consisted of a two LC-20AD pumps (Shimadzu, Japan), an automatic sample injector, coupled on-line with an LCMS-IT-TOF (Shimadzu, Japan) mass spectrometer. The column effluent was analyzed by ESI-MS. MS detection was operated in positive ionisation mode with the following parameters: detector voltage, 1.53 kV; interface voltage, +4.5 kV; CDL (curve desolvation line) temperature, 200 ˚C; block heater temperature, 200 ˚C; nebulizing gas flow (He), 1.5 L/min; drying gas pressure, 100 kPa. Full scan MS data were acquired in the range of 80–850 m/z (ion accumulation time, 30 ms; event time, 300 ms; repeat = 3.
Ion Mode:POSITIVE
Capillary Voltage:+4.5 kV
Dry Gas Flow:100 kPa
Helium Flow:1.5 ml/min
Ion Source Temperature:200 ˚C
Ionization:positive
Mass Accuracy:15 ppm
Source Temperature:200 ˚C
Cdl Temperature:200 ˚C
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