Summary of Study ST000081

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.

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Study IDST000081
Study TitleMetabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Cancer Patients: UHPLC-QTOF MS analyis of subcutaneous and visceral adipose tissue 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 Groups2
Total Subjects59
Study CommentsLipidomics profiles for study
This is the SAT and VAT part of the study
Label-ID os conserved for all parts of the study
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The samples had to be diluted for positive mode measurements (therefore 2 dilutions are measured for the same sample). Results are then combined and scaling factor is used for final results.
Raw Data AvailableYes
Raw Data File Type(s)d
Uploaded File Size31 G
Analysis Type DetailLC-MS
Release Date2014-07-26
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:SU000100
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Tissue type
SA004063QC 02Adipose Tissue_QC
SA004064QC 03Adipose Tissue_QC
SA004065QC 04Adipose Tissue_QC
SA004066QC 05Adipose Tissue_QC
SA004067QC 06Adipose Tissue_QC
SA004068QC01Adipose Tissue_QC
SA004069SAT_57Subcutaenous Adipose
SA004070SAT_20Subcutaenous Adipose
SA004071SAT_28Subcutaenous Adipose
SA004072SAT_31Subcutaenous Adipose
SA004073SAT_10Subcutaenous Adipose
SA004074SAT_23Subcutaenous Adipose
SA004075SAT_27Subcutaenous Adipose
SA004076SAT_38Subcutaenous Adipose
SA004077SAT_16Subcutaenous Adipose
SA004078SAT_4Subcutaenous Adipose
SA004079SAT_37Subcutaenous Adipose
SA004080SAT_58Subcutaenous Adipose
SA004081SAT_15Subcutaenous Adipose
SA004082SAT_22Subcutaenous Adipose
SA004083SAT_14Subcutaenous Adipose
SA004084SAT_33Subcutaenous Adipose
SA004085SAT_30Subcutaenous Adipose
SA004086SAT_56Subcutaenous Adipose
SA004087SAT_34Subcutaenous Adipose
SA004088SAT_13Subcutaenous Adipose
SA004089SAT_48Subcutaenous Adipose
SA004090SAT_41Subcutaenous Adipose
SA004091SAT_39Subcutaenous Adipose
SA004092SAT_6Subcutaenous Adipose
SA004093SAT_25Subcutaenous Adipose
SA004094SAT_46Subcutaenous Adipose
SA004095SAT_59Subcutaenous Adipose
SA004096SAT_3Subcutaenous Adipose
SA004097SAT_18Subcutaenous Adipose
SA004098SAT_32Subcutaenous Adipose
SA004099SAT_7Subcutaenous Adipose
SA004100SAT_29Subcutaenous Adipose
SA004101SAT_50Subcutaenous Adipose
SA004102SAT_2Subcutaenous Adipose
SA004103SAT_8Subcutaenous Adipose
SA004104SAT_54Subcutaenous Adipose
SA004105SAT_12Subcutaenous Adipose
SA004106SAT_11Subcutaenous Adipose
SA004107SAT_49Subcutaenous Adipose
SA004108SAT_19Subcutaenous Adipose
SA004109SAT_35Subcutaenous Adipose
SA004110SAT_55Subcutaenous Adipose
SA004111SAT_44Subcutaenous Adipose
SA004112SAT_40Subcutaenous Adipose
SA004113SAT_17Subcutaenous Adipose
SA004114SAT_36Subcutaenous Adipose
SA004115SAT_43Subcutaenous Adipose
SA004116SAT_47Subcutaenous Adipose
SA004117SAT_53Subcutaenous Adipose
SA004118SAT_26Subcutaenous Adipose
SA004119SAT_5Subcutaenous Adipose
SA004120SAT_24Subcutaenous Adipose
SA004121SAT_51Subcutaenous Adipose
SA004122SAT_21Subcutaenous Adipose
SA004123SAT_1Subcutaenous Adipose
SA004124SAT_42Subcutaenous Adipose
SA004125SAT_45Subcutaenous Adipose
SA004126SAT_9Subcutaenous Adipose
SA004127SAT_52Subcutaenous Adipose
SA004128VAT_5Visceral Adipose
SA004129VAT_56Visceral Adipose
SA004130VAT_2Visceral Adipose
SA004131VAT_33Visceral Adipose
SA004132VAT_19Visceral Adipose
SA004133VAT_48Visceral Adipose
SA004134VAT_34Visceral Adipose
SA004135VAT_4Visceral Adipose
SA004136VAT_9Visceral Adipose
SA004137VAT_52Visceral Adipose
SA004138VAT_35Visceral Adipose
SA004139VAT_50Visceral Adipose
SA004140VAT_55Visceral Adipose
SA004141VAT_37Visceral Adipose
SA004142VAT_29Visceral Adipose
SA004143VAT_38Visceral Adipose
SA004144VAT_43Visceral Adipose
SA004145VAT_36Visceral Adipose
SA004146VAT_21Visceral Adipose
SA004147VAT_14Visceral Adipose
SA004148VAT_25Visceral Adipose
SA004149VAT_40Visceral Adipose
SA004150VAT_54Visceral Adipose
SA004151VAT_20Visceral Adipose
SA004152VAT_49Visceral Adipose
SA004153VAT_13Visceral Adipose
SA004154VAT_28Visceral Adipose
SA004155VAT_53Visceral Adipose
SA004156VAT_47Visceral Adipose
SA004157VAT_24Visceral Adipose
SA004158VAT_3Visceral Adipose
SA004159VAT_57Visceral Adipose
SA004160VAT_27Visceral Adipose
SA004161VAT_12Visceral Adipose
SA004162VAT_32Visceral Adipose
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Collection:

Collection ID:CO000083
Collection Summary:-
Collection Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf
Sample Type:Adipose tissue:

Treatment:

Treatment ID:TR000101
Treatment Summary:Adipose tissue:
(1) Subcutaenous Adipose
(2) Visceral Adipose
Treatment Protocol Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics.pdf

Sample Preparation:

Sampleprep ID:SP000096
Sampleprep Summary:-
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 AN000131 AN000132
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:CH000092
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% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate
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:MS000107
Analysis ID:AN000131
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:MS000108
Analysis ID:AN000132
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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