Summary of Study ST001271

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 PR000857. The data can be accessed directly via it's Project DOI: 10.21228/M8X110 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 IDST001271
Study TitleColorectal cancer before and after surgery metabolomics data integration
Study TypePilot study
Study SummaryIn this study 40 urine samples were analyzed in 5 batches. There are 3 labels: control group volunteers (8 pcs., CG), colorectal cancer patients before surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post).
Institute
Lomonosov MSU
DepartmentChemistry
LaboratoryMass spectrometry
Last NamePlyushchenko
First NameIvan
AddressLeninskie gory, 1/3
Emailplyush1993@bk.ru
Phone89160362200
Submit Date2019-10-29
Analysis Type DetailLC-MS
Release Date2020-01-13
Release Version1
Ivan Plyushchenko Ivan Plyushchenko
https://dx.doi.org/10.21228/M8X110
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000857
Project DOI:doi: 10.21228/M8X110
Project Title:Colorectal cancer before and after surgery metabolomics data integration
Project Type:Pilot study
Project Summary:In this study 40 urine samples were analyzed in 5 batches. There are 3 labels: control group volunteers (8 pcs., CG), colorectal cancer patients before surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post).
Institute:Lomonosov Moscow State University
Department:Chemistry
Laboratory:Mass spectrometry
Last Name:Plyushchenko
First Name:Ivan
Address:Leninskie gory, 1/3, Moscow, Moscow, 119234, Russian Federation
Email:plyush1993@bk.ru
Phone:+79160362200
Publications:Plyushchenko Ivan, et al. "An approach for feature selection with data modelling in LC-MS metabolomics." Analytical Methods 12.28 (2020): 3582-3591. DOI: 10.1039/d0ay00204f
Contributors:Rodin I., Shakhmatov D., Bolotnik T.

Subject:

Subject ID:SU001339
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Treatment
SA09238322CGCG
SA09238426CGCG
SA09238525CGCG
SA09238627CGCG
SA09238724CGCG
SA09238828CGCG
SA09238923CGCG
SA09239029CGCG
SA09239111postpost
SA09239219postpost
SA09239310postpost
SA09239421postpost
SA09239520postpost
SA0923966postpost
SA0923972postpost
SA0923981postpost
SA09239918postpost
SA0924003postpost
SA0924015postpost
SA0924024postpost
SA09240319prepre
SA09240420prepre
SA09240521prepre
SA09240615prepre
SA0924076prepre
SA0924087prepre
SA0924098prepre
SA0924105prepre
SA0924114prepre
SA0924122prepre
SA0924133prepre
SA0924149prepre
SA09241511prepre
SA09241616prepre
SA09241717prepre
SA0924181prepre
SA09241914prepre
SA09242012prepre
SA09242113prepre
SA09242218prepre
Showing results 1 to 40 of 40

Collection:

Collection ID:CO001333
Collection Summary:40 urine samples were analyzed in 5 batches. There are 3 labels: control group volunteers (8 pcs., CG), colorectal cancer patients before surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post).
Sample Type:Urine
Storage Conditions:-20℃

Treatment:

Treatment ID:TR001354
Treatment Summary:All morning fasting urine samples (on an empty stomach, immediately after sleep) from the State Scientific Center of Coloproctology (Moscow, Russia) were collected in sterilized plastic sealed falcons for this study and were frozen in the refrigerator at -20 °C. Then the samples in containers with cold cells were transported to the laboratory. In control group patients with fistula, hemorrhoid, diverticulosis, irritable bowel syndrome and anal fissure were included. In the sample group after the operation, samples were collected no more than three days after the operation. In the sample group before the operation, patients with different histological stages (G1-G3) were involved. The age and sex of the collected subjects were matched as much as possible. All the samples were stored at -24 ˚C until analysis and were defrosted at room temperature prior the analysis.

Sample Preparation:

Sampleprep ID:SP001347
Sampleprep Summary:Prior to analysis, samples were defrosted at room temperature 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 and centrifuged at 16000 rpm for 15 min and then aliquots of supernatant were placed into vials.

Combined analysis:

Analysis ID AN002111
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column ACQUITY UPLC BEH C18 (1.7 µm, 2.1 mm X 5 mm);Agilent ZORBAX StableBond C18 UHPLC guard (4.6 mm, 1.8 µm)
MS Type ESI
MS instrument type Other
MS instrument name Shimadzu LCMS-IT-TOF
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH001541
Chromatography Summary:Two solvents were used: (A) deionized water with 0,1% formic acid, and (B) MeCN. After a 5 min hold at 5.0% solvent B, elution was performed according to the following conditions: from 5.0% B to 59% B in 30 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. The flow rate was 0.3 mL•min-1. The injection volume was 5 μL.
Chromatography Comments:Acquity UPLC BEH; 1.7 μm 2.1 × 5 mm UHPLC Guard 3PK Zorbax SB-C18 1.8 μm guard column
Instrument Name:Shimadzu 20AD
Column Name:ACQUITY UPLC BEH C18 (1.7 µm, 2.1 mm X 5 mm);Agilent ZORBAX StableBond C18 UHPLC guard (4.6 mm, 1.8 µm)
Column Pressure:300-500 bar
Column Temperature:30
Flow Gradient:non-linear
Flow Rate:0.3 ml/min
Injection Temperature:5
Internal Standard:papaverine
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS001962
Analysis ID:AN002111
Instrument Name:Shimadzu LCMS-IT-TOF
Instrument Type:Other
MS Type:ESI
MS Comments:Mass range: 100 – 850 Da (SCAN mode). Other MS parameters were default (manufacturer recommendations).
Ion Mode:POSITIVE
Capillary Voltage:1.55 kV
Dry Gas Flow:100 kPa
Source Temperature:200
Cdl Temperature:200
Interface Voltage:4.5 kV
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