Summary of Study ST002341

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 PR001503. The data can be accessed directly via it's Project DOI: 10.21228/M8DQ5R 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 IDST002341
Study TitleMetabolomic analysis of colorectal cancer cells using mass spectrometry
Study SummaryColorectal cancer (CRC) is one of the most prevalent tumors, with a high mortality rate. Nearly half of CRC patients develop metastasis, which accounts for as many as 90% of CRC-related deaths. In the metastasis process, cancer cells exhibit altered dependency on specific metabolic pathways and some of the metabolites discovered might be useful as potential diagnostic biomarkers. To identify metabolic pathway dependencies in CRC metastasis, mass spectrometry-based untargeted metabolomic analysis was performed in two pairs of CRC cell lines with different metastatic abilities. Each pair of cell lines was comprised of primary and metastatic colorectal cancer cell lines (SW480 vs. SW620; HT-29 vs. COLO 205). Relative levels of intracellular metabolites distinguished high-metastatic CRC cells from low-metastatic CRC cells.
Institute
Nanjing Medical University
Last NameZhang
First NameWenjun
Address101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China
Emailzwj941027369@163.com
Phone+86-025-86868326
Submit Date2022-10-06
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-28
Release Version1
Wenjun Zhang Wenjun Zhang
https://dx.doi.org/10.21228/M8DQ5R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001503
Project DOI:doi: 10.21228/M8DQ5R
Project Title:Metabolomic analysis of colorectal cancer cells using mass spectrometry
Project Summary:Two pairs of human colorectal cancer cell lines with different metastatic abilities (SW480 vs SW620, HT-29 vs COLO-205) were used to screen differential metabolites.
Institute:Nanjing Medical University
Last Name:Zhang
First Name:Wenjun
Address:101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China
Email:zwj941027369@163.com
Phone:+86-025-86868326

Subject:

Subject ID:SU002430
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Class
SA235097Blank_pos_04Blank
SA235098Blank_pos_03Blank
SA235099Blank_pos_02Blank
SA235100Blank_pos_05Blank
SA235101Blank_pos_06Blank
SA235102Blank_pos_08Blank
SA235103Blank_pos_07Blank
SA235104Blank_neg_01Blank
SA235105Blank_pos_01Blank
SA235106Blank_neg_06Blank
SA235107Blank_neg_07Blank
SA235108Blank_neg_04Blank
SA235109Blank_neg_03Blank
SA235110Blank_neg_02Blank
SA235111Blank_neg_08Blank
SA235112Blank_neg_05Blank
SA235113COLO205_pos_08High metastatic ability
SA235114COLO205_neg_09High metastatic ability
SA235115COLO205_pos_07High metastatic ability
SA235116COLO205_pos_06High metastatic ability
SA235117COLO205_pos_05High metastatic ability
SA235118COLO205_neg_08High metastatic ability
SA235119COLO205_neg_07High metastatic ability
SA235120COLO205_neg_03High metastatic ability
SA235121COLO205_neg_02High metastatic ability
SA235122COLO205_neg_04High metastatic ability
SA235123COLO205_neg_05High metastatic ability
SA235124COLO205_neg_06High metastatic ability
SA235125COLO205_pos_04High metastatic ability
SA235126COLO205_pos_03High metastatic ability
SA235127SW620_pos_06High metastatic ability
SA235128SW620_pos_05High metastatic ability
SA235129SW620_pos_07High metastatic ability
SA235130SW620_pos_08High metastatic ability
SA235131SW620_pos_09High metastatic ability
SA235132SW620_pos_04High metastatic ability
SA235133SW620_pos_03High metastatic ability
SA235134COLO205_pos_02High metastatic ability
SA235135COLO205_pos_01High metastatic ability
SA235136SW620_pos_01High metastatic ability
SA235137SW620_pos_02High metastatic ability
SA235138COLO205_neg_01High metastatic ability
SA235139COLO205_pos_09High metastatic ability
SA235140SW620_neg_01High metastatic ability
SA235141SW620_neg_06High metastatic ability
SA235142SW620_neg_07High metastatic ability
SA235143SW620_neg_05High metastatic ability
SA235144SW620_neg_04High metastatic ability
SA235145SW620_neg_02High metastatic ability
SA235146SW620_neg_03High metastatic ability
SA235147SW620_neg_08High metastatic ability
SA235148SW620_neg_09High metastatic ability
SA235149SW480_pos_09Low metastatic ability
SA235150HT29_pos_04Low metastatic ability
SA235151HT29_pos_03Low metastatic ability
SA235152SW480_pos_08Low metastatic ability
SA235153SW480_pos_07Low metastatic ability
SA235154SW480_pos_05Low metastatic ability
SA235155SW480_pos_06Low metastatic ability
SA235156HT29_pos_02Low metastatic ability
SA235157HT29_pos_01Low metastatic ability
SA235158SW480_pos_04Low metastatic ability
SA235159SW480_neg_09Low metastatic ability
SA235160SW480_neg_08Low metastatic ability
SA235161SW480_neg_06Low metastatic ability
SA235162SW480_neg_05Low metastatic ability
SA235163SW480_neg_03Low metastatic ability
SA235164SW480_neg_04Low metastatic ability
SA235165SW480_neg_07Low metastatic ability
SA235166HT29_pos_07Low metastatic ability
SA235167HT29_neg_03Low metastatic ability
SA235168HT29_neg_02Low metastatic ability
SA235169HT29_pos_05Low metastatic ability
SA235170HT29_neg_04Low metastatic ability
SA235171HT29_neg_05Low metastatic ability
SA235172HT29_neg_08Low metastatic ability
SA235173HT29_neg_07Low metastatic ability
SA235174HT29_neg_06Low metastatic ability
SA235175SW480_pos_03Low metastatic ability
SA235176SW480_neg_01Low metastatic ability
SA235177HT29_pos_06Low metastatic ability
SA235178SW480_pos_01Low metastatic ability
SA235179SW480_pos_02Low metastatic ability
SA235180HT29_neg_09Low metastatic ability
SA235181HT29_pos_08Low metastatic ability
SA235182SW480_neg_02Low metastatic ability
SA235183HT29_pos_09Low metastatic ability
SA235184HT29_neg_01Low metastatic ability
SA235185QC_neg_04QC
SA235186QC_pos_01QC
SA235187QC_neg_03QC
SA235188QC_neg_06QC
SA235189QC_neg_07QC
SA235190QC_neg_08QC
SA235191QC_neg_02QC
SA235192QC_neg_01QC
SA235193QC_neg_05QC
SA235194QC_pos_02QC
SA235195QC_pos_06QC
SA235196QC_pos_07QC
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Collection:

Collection ID:CO002423
Collection Summary:Two hours before metabolite extraction, the cell culture medium was replaced with fresh medium. After discarding the medium in each culture dish, the cells were quickly rinsed twice with cold isotonic saline (0.9% NaCl [w/v], 4 °C). Water (1.5 mL) was added to each dish, and then the dishes were stored in a freezer (−80 °C) for 20 min before extraction.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR002442
Treatment Summary:SW480 cells and SW620 cells were cultured in DMEM medium supplemented with 10% FBS at 37 °C under a 5% CO2 atmosphere, HT-29 and COLO 205 cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37 °C under a 5% CO2 atmosphere.
Cell Media:DMEM medium supplemented with 10% FBS is for SW480 cells and SW620 cells, while RPMI 1640 medium supplemented with 10% FBS is for HT-29 and COLO 205 cells.
Cell Envir Cond:at 37 °C under a 5% CO2 atmosphere
Cell Harvesting:After discarding the medium in each culture dish, the cells were quickly rinsed twice with cold isotonic saline (0.9% NaCl [w/v], 4 °C). Water (1.5 mL) was added to each dish, and then the dishes were stored in a freezer (−80 °C) for 20 min before extraction. Then, cells were collected by scraping with a cell scraper.
Cell Pct Confluence:70%-80%

Sample Preparation:

Sampleprep ID:SP002436
Sampleprep Summary:Cell lysates (20 μL) were removed for a protein assay, and the remaining cell lysates were extracted by the addition of 4.5 mL of methanol containing 3 μg of internal standard (acetaminophen). The cells were completely collected with a cell scraper. Finally, the suspension of cell debris in each dish was transferred to an Eppendorf tube, vigorously vortexed for 5 min, and then centrifuged at 10,000×g for 10 min at 4 °C. The supernatant was transferred to another tube and evaporated to dryness in a Refrigerated CentriVap Benchtop Vacuum Concentrator (Labconco Corporation, Kansas City, MO). The pellets were reconstituted with methanol-water (75:25) and centrifuged twice at 12,000×g for 15 min at 4 °C.

Combined analysis:

Analysis ID AN003824 AN003825
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system UPLC Ultimate 3000 system UPLC Ultimate 3000 system
Column Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) Phenomenex Kinetex C18 (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH002830
Instrument Name:UPLC Ultimate 3000 system
Column Name:Phenomenex Kinetex C18 (100 x 2.1mm,2.6um)
Column Temperature:40 °C
Flow Gradient:10% B (0 min) → 30% B (1 min) → 95% B (19 min) → 95% B (20 min)
Flow Rate:0.4 mL/min
Injection Temperature:4 °C
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003566
Analysis ID:AN003824
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard).
Ion Mode:POSITIVE
Capillary Temperature:300 °C
Capillary Voltage:+3.5 kV
  
MS ID:MS003567
Analysis ID:AN003825
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard).
Ion Mode:NEGATIVE
Capillary Temperature:300 °C
Capillary Voltage:-2.5 kV
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