Summary of study ST000082

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 PR000058. The data can be accessed directly via it's Project DOI: 10.21228/M80018 This work is supported by NIH grant, U2C- DK119886.

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

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Study IDST000082
Study TitleMetabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Cancer Patients: UHPLC-QTOF MS analyis of serum samples
Study Typebiomarker study
Study SummaryThis West Coast Metabolomics Center pilot and feasibility project was granted to Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, Seattle). In the current investigation, unbiased profiling of the metabolome and lipidome of adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 CRC patients, including stages I-IV, from the Fred Hutchinson Cancer Center (Seattle,WA) and the German Cancer Research Center (Heidelberg, Germany) was conducted. The lipidome and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using established UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively.  The primary objectives of this project were to 1) compare the metabolome and lipidome of matched VAT and SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) characterize the associations between the lipidome and metabolome in adipose tissue (VAT/SAT) and serum of n=50 CRC patients and 3) test the associations between the lipidome/metabolome of VAT and serum with the tumor stage of CRC patients. 
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility 451 Health Sciences Drive Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2014-06-11
Num Groups1
Total Subjects59
Study CommentsLipidomics profiles for study
This is the serum part of the study
Label-ID os conserved for all parts of the study
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Raw Data AvailableYes
Raw Data File Type(s).cd,.cG,.bin,.xml,.stg
Uploaded File Size14 G
Analysis Type DetailLC-MS
Release Date2014-07-25
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M80018
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000058
Project DOI:doi: 10.21228/M80018
Project Title:Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Cancer Patients: Unraveling the Link Between Adipose Tissue and Cancer
Project Type:biomarker study
Project Summary:This West Coast Metabolomics Center pilot and feasibility project was granted to Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, Seattle). In the current investigation, unbiased profiling of the metabolome and lipidome of adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 CRC patients, including stages I-IV, from the Fred Hutchinson Cancer Center (Seattle,WA) and the German Cancer Research Center (Heidelberg, Germany) was conducted. The lipidome and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using established UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary objectives of this project were to 1) compare the metabolome and lipidome of matched VAT and SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) characterize the associations between the lipidome and metabolome in adipose tissue (VAT/SAT) and serum of n=50 CRC patients and 3) test the associations between the lipidome/metabolome of VAT and serum with the tumor stage of CRC patients.
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
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154

Subject:

Subject ID:SU000101
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Source
SA004190QC01Pooled Plasma
SA004191QC02Pooled Plasma
SA004192QC03Pooled Plasma
SA004193S43Serum
SA004194S42Serum
SA004195S44Serum
SA004196S45Serum
SA004197S46Serum
SA004198S41Serum
SA004199S37Serum
SA004200S36Serum
SA004201S35Serum
SA004202S47Serum
SA004203S38Serum
SA004204S39Serum
SA004205S40Serum
SA004206S51Serum
SA004207S57Serum
SA004208S56Serum
SA004209S58Serum
SA004210S59Serum
SA004211Pooled MSMS.dSerum
SA004212S55Serum
SA004213S54Serum
SA004214S50Serum
SA004215S49Serum
SA004216S34Serum
SA004217S52Serum
SA004218S53Serum
SA004219S48Serum
SA004220S33Serum
SA004221S12Serum
SA004222S11Serum
SA004223S10Serum
SA004224S13Serum
SA004225S14Serum
SA004226S16Serum
SA004227S15Serum
SA004228S9Serum
SA004229S8Serum
SA004230S3Serum
SA004231S2Serum
SA004232S4Serum
SA004233S5Serum
SA004234S7Serum
SA004235S6Serum
SA004236S17Serum
SA004237S18Serum
SA004238S28Serum
SA004239S27Serum
SA004240S29Serum
SA004241S30Serum
SA004242S32Serum
SA004243S31Serum
SA004244S26Serum
SA004245S25Serum
SA004246S20Serum
SA004247S19Serum
SA004248S21Serum
SA004249S22Serum
SA004250S24Serum
SA004251S23Serum
SA004252S1Serum
Showing results 1 to 63 of 63

Collection:

Collection ID:CO000084
Collection Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Sample Type:Human serum

Treatment:

Treatment ID:TR000102
Treatment Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf

Sample Preparation:

Sampleprep ID:SP000097
Sampleprep Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Subcutaneous_and_Visceral_Fat_Extraction_Protocol.docx
Sampleprep Protocol Comments:see Subcutaneous and Visceral Fat Extraction Protocol.docx

Combined analysis:

Analysis ID AN000133 AN000134
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH000094
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Instrument Name:Waters Acquity
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Internal Standard:See data dictionary
Retention Time:See data dictionary
Sample Injection:1.67 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000109
Analysis ID:AN000133
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000110
Analysis ID:AN000134
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 l/min
Dry Gas Temp:200
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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