Summary of Study ST000054

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000051. The data can be accessed directly via it's Project DOI: 10.21228/M8MS3J This work is supported by NIH grant, U2C- DK119886.


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 IDST000054
Study TitleMetabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis)
Study TypeMetabolomic analysis of normal breast tissue
Study SummaryThe purpose of this study was to understand the metabolomic changes in a breast tissue microenvironment at various stages of cancer development and progression (i.e. normal breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and feasibility study was to apply a broad spectrum GC-MS metabolomics method to determine whether changes in normal tissue of women with cancer correlate with progression and or the subtype of the disease.
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Submit Date2014-04-30
Num Groups8
Total Subjects192
Study Commentssample preparation and analysis randomized with data collection over multiple days
Publications1. Brauer HA, Makowski L, Hoadley KA, Casbas-Hernandez P, Lang LJ, Roman-Perez E, D’Arcy M, Freemerman AJ, Perou CM, Troester MA: Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer. Clin Cancer Res 2012;19:571-585. 2. J Budczies, C Denkert, B Muller, S Brockmoller, F Klauschen, B Gyorffy, M Dietel, C Richter-Ehrenstein, U Marten, R Salek, J Griffin, M Hilvo, M Oresic, G Wohlgemuth, O Fiehn: Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue – a GC-TOFMS based metabolomics study. BMC Genomics 2012; 13:334.
Raw Data AvailableYes
Raw Data File Type(s)cdf
Uploaded File Size8.4 G
Analysis Type DetailGC-MS
Release Date2018-08-27
Release Version1
Susan Sumner Susan Sumner application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000051
Project DOI:doi: 10.21228/M8MS3J
Project Title:Metabolic Microenvironments in Normal Breast and Breast Cancer
Project Type:Broad Spectrum
Project Summary:Breast cancers evolve and acquire adaptive changes while in active communication with the surrounding host normal tissue. It is important to understand the genomic and metabolomic changes in breast microenvironment at various stages of cancer development and progression (i.e., normal breast, DCIS, benign disease and invasive cancer). Since intrinsic breast cancer subtypes are very distinct from each other in terms of clinical features as well as the genomic profiling, these subtypes may also have distinct metabolic microenvironment signatures.
Institute:University of North Carolina at Chapel Hill
Laboratory:Troester Laboratory
Last Name:Troester
First Name:Melissa
Address:University of North Carolina at Chapel Hill Chapel Hill, NC 27599


Subject ID:SU000073
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human


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

mb_sample_id local_sample_id treatment pool aliquot
SA0026291402110jcsa35_1Basal no
SA002630140217ajcsa17_1Basal no
SA002631140214ajcsa10_1Basal no
SA002632140217ajcsa46_1Basal no
SA002633140219ajcsa08_1Basal no
SA002634140219ajcsa38_1Basal no
SA0026351402110jcsa37_1Basal no
SA002636140217ajcsa16_1Basal no
SA002637140214ajcsa40_1Basal no
SA002638140214ajcsa08_1Basal no
SA002639140214ajcsa44_1Basal no
SA002640140217ajcsa09_1Basal no
SA0026411402110jcsa42_1Basal no
SA0026421402110jcsa19_1Basal no
SA002643140214ajcsa28_1Basal no
SA002644140219ajcsa19_1Basal no
SA002645140219ajcsa24_1Basal no
SA0026461402110jcsa12_1Basal no
SA002647140219ajcsa22_1Basal no
SA002648140219ajcsa28_1Basal no
SA002649140219ajcsa36_1Basal no
SA002650140217ajcsa36_1Basal yes
SA0026511402110jcsa44_1Basal yes
SA002652140214ajcsa35_1Basal yes
SA002653140219ajcsa26_1Basal yes
SA002654140219ajcsa45_1DCIS no
SA002655140214ajcsa45_1DCIS no
SA002656140214ajcsa17_1DCIS no
SA002657140217ajcsa10_1DCIS no
SA0026581402110jcsa07_1DCIS no
SA002659140217ajcsa11_1DCIS no
SA002660140219ajcsa32_1DCIS no
SA002661140219ajcsa51_1DCIS no
SA002662140214ajcsa39_1DCIS no
SA002663140219ajcsa17_1DCIS no
SA002664140219ajcsa54_1DCIS no
SA002665140214ajcsa43_1DCIS no
SA002666140219ajcsa50_1DCIS no
SA002667140217ajcsa45_1DCIS no
SA002668140217ajcsa12_1DCIS no
SA002669140219ajcsa14_1DCIS no
SA002670140214ajcsa22_1DCIS no
SA0026711402110jcsa32_1DCIS no
SA002672140217ajcsa26_1DCIS no
SA002673140214ajcsa16_1DCIS no
SA0026741402110jcsa17_1DCIS no
SA002675140214ajcsa33_1DCIS no
SA002676140214ajcsa31_1DCIS no
SA002677140219ajcsa29_1DCIS no
SA002678140219ajcsa40_1DCIS no
SA002679140214ajcsa36_1DCIS yes
SA002680140217ajcsa19_1DCIS yes
SA0026811402110jcsa23_1DCIS yes
SA002682140219ajcsa10_1DCIS yes
SA002683140214ajcsa23_1HER2 no
SA002684140217ajcsa21_1HER2 no
SA002685140219ajcsa21_1HER2 no
SA002686140219ajcsa31_1HER2 no
SA002687140219ajcsa18_1HER2 no
SA002688140217ajcsa33_1HER2 no
SA002689140217ajcsa15_1HER2 no
SA002690140217ajcsa28_1HER2 no
SA002691140217ajcsa14_1HER2 no
SA002692140214ajcsa42_1HER2 no
SA002693140214ajcsa12_1HER2 no
SA0026941402110jcsa36_1HER2 no
SA0026951402110jcsa45_1HER2 no
SA0026961402110jcsa46_1HER2 no
SA0026971402110jcsa43_1HER2 no
SA0026981402110jcsa28_1HER2 no
SA002699140214ajcsa21_1HER2 yes
SA002700140219ajcsa16_1HER2 yes
SA0027011402110jcsa47_1HER2 yes
SA002702140217ajcsa30_1HER2 yes
SA002703140217ajcsa37_1LumA no
SA002704140217ajcsa47_1LumA no
SA0027051402110jcsa10_1LumA no
SA002706140219ajcsa42_1LumA no
SA0027071402110jcsa26_1LumA no
SA002708140217ajcsa07_1LumA no
SA002709140217ajcsa18_1LumA no
SA0027101402110jcsa14_1LumA no
SA002711140217ajcsa29_1LumA no
SA0027121402110jcsa29_1LumA no
SA002713140217ajcsa24_1LumA no
SA0027141402110jcsa33_1LumA no
SA002715140214ajcsa47_1LumA no
SA002716140217ajcsa43_1LumA no
SA002717140219ajcsa23_1LumA no
SA0027181402110jcsa39_1LumA no
SA002719140219ajcsa43_1LumA no
SA002720140214ajcsa11_1LumA no
SA0027211402110jcsa25_1LumA no
SA0027221402110jcsa21_1LumA no
SA002723140219ajcsa12_1LumA no
SA0027241402110jcsa18_1LumA no
SA002725140219ajcsa55_1LumA no
SA002726140217ajcsa42_1LumA yes
SA002727140214ajcsa15_1LumA yes
SA002728140219ajcsa30_1LumA yes
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Collection ID:CO000056
Collection Summary:Cancer-adjacent, normal breast tissue was collected
Collection Protocol ID:UNC-CH IRB #09-1436
Collection Protocol Filename:Normal_Breast_Study
Collection Protocol Comments:Breast tissue samples were collected from patients in the UNC hospital system under the Normal Breast Study (IRB #09-1436). Normal breast tissue from patients with reduction mammoplasty, DCIS and invasive breast cancer were analyzed in this study. Tissue samples 2-4 cm away from the tumor were collected and stored at -80°C after surgery. Samples were cut on dry ice to yield a metabolomics sample comprising 50-120 mg tissue. The tissue was placed in a tissue homogenization tube with ceramic beads and stored at -80°C. The samples were delivered to the RTI RCMRC and stored at -80°C.
Sample Type:tissue
Collection Method:tissue collected during surgery
Collection Location:breast microenvironment
Collection Frequency:one time collection
Volumeoramount Collected:50 - 120mg
Storage Conditions:-80 C
Tissue Cell Identification:breast
Tissue Cell Quantity Taken:50mg


Treatment ID:TR000074
Treatment Summary:Stages of breast cancer progression and different subtypes compared to a non-malignant control
Treatment Protocol Comments:DCIS, Luminal A, Luminal B, HER2, Basal, Reduction, Total Pool1 (equal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples),Total Pool2 (unequal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples)

Sample Preparation:

Sampleprep ID:SP000069
Sampleprep Summary:Breast tissue samples were homogenized in 3:3:2 (acetonitrile:isopropanol:water) at a concentration of 100 mg/mL. Samples dried and extracted into 50% acetonitrile. Sample dried and aliquot taken for NMR. Sample returned and extract processed for GC/MS analysis. Samples were derivatized using 2 step derivatization method (methoximation with methoxy amine followed by TMS derivatization with MSTFA).
Sampleprep Protocol Filename:RTI_MT_Breast_Tissue_Procedures_GC-TOF-MS.docx
Processing Method:Homogenization and Solvent Removal with SpeedVac
Processing Storage Conditions:4°C
Extraction Method:3:3:2 (acetonitrile:isopropanol:water) and then 50% Acetonitrile
Extract Concentration Dilution:dried on SpeedVac
Extract Storage:-80°C
Sample Resuspension:resuspended in D2O + Chenomix ISTD solution
Sample Derivatization:Methoximation with methoxy amine at 40 mg/ml in pyridine followed by TMS derivatization with MSTFA
Sample Spiking:FAMES (C8-C30) added to MSTFA as retention time markers

Combined analysis:

Analysis ID AN000092
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus 4D GC
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus 4D GCxGC TOF
Units Peak height


Chromatography ID:CH000060
Chromatography Summary:GC/MS analysis is based on Oliver Fiehn methods
Instrument Name:Leco Pegasus 4D GC
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Column Pressure:10.4 psi
Column Temperature:50C(0.5 min)-330C(@20C/min)-330C(5 min)
Flow Gradient:constant flow
Flow Rate:1.0 mL/min
Injection Temperature:250C
Retention Index:FAMEs markers (C8-C30)
Retention Time:FAMEs markers (C8-C30)
Analytical Time:20 minutes
Oven Temperature:50C(0.5 min)-330C(@20C/min)-330C(5 min)
Transferline Temperature:280C
Sample Syringe Size:10 L
Chromatography Type:GC


MS ID:MS000069
Analysis ID:AN000092
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Capillary Temperature:280C (transfer line)
Helium Flow:1.0 ml/min
Ion Source Temperature:250C
Ionization Energy:70 eV
Source Temperature:250C
Resolution Setting:1200
Scan Range Moverz:50-800
Scanning:20 spectra/sec