Summary of Study ST000356

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 PR000284. The data can be accessed directly via it's Project DOI: 10.21228/M86K6W This work is supported by NIH grant, U2C- DK119886.


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Study IDST000356
Study TitleGC/MS and LC/MS metabolomics profiling for breast cancer serum data and control serum data
Study Typemetabolomics profiling
Study SummaryUse GC/MS and LC/MS technique to profile breast cancer samples and normal control samples
University of Hawaii
DepartmentCancer Center
LaboratoryMetabolomics Shared Resource
Last NameXie
First NameGuoxiang
Phone(808) 564-5938
Submit Date2016-03-09
Raw Data File Type(s)d, raw
Analysis Type DetailGC-MS/LC-MS
Release Date2016-03-21
Release Version1
Guoxiang Xie Guoxiang Xie application/zip

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Project ID:PR000284
Project DOI:doi: 10.21228/M86K6W
Project Title:Breast Cancer GC/MS and LC/MS plasma data from City of Hope Hospital
Project Type:GC/MS and LC/MS metabolomics profiling
Project Summary:Breast cancer diagnosis profiling
Institute:University of Hawaii
Department:Metabolomics Shared Resource, Cancer Center
Last Name:Xie
First Name:Guoxiang
Phone:(808) 564-5938


Subject ID:SU000377
Subject Type:Human breast cancer and normal controls serum metabolomics profiling
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human


Subject type: Human breast cancer and normal controls serum metabolomics profiling; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Diagnosis stage
SA01574737_1breast cancer -
SA015748123_1breast cancer -
SA01574943_1breast cancer -
SA01575084_1breast cancer -
SA01575150_1breast cancer -
SA01575280_1breast cancer -
SA015753128_1breast cancer 2
SA015754117_1breast cancer 2
SA015755129_1breast cancer 2
SA015756119_1breast cancer 2
SA015757136_1breast cancer 2
SA015758113_1breast cancer 2
SA015759143_1breast cancer 2
SA015760140_1breast cancer 2
SA015761134_1breast cancer 2
SA015762107_1breast cancer 2
SA01576398_1breast cancer 2
SA01576429_1breast cancer 2
SA01576515_1breast cancer 2
SA015766104_1breast cancer 2
SA01576719_1breast cancer 2
SA015768110_1breast cancer 2
SA01576911_1breast cancer 2
SA015770111_1breast cancer 2
SA01577133_1breast cancer 2
SA01577281_1breast cancer 2
SA01577371_1breast cancer 2
SA01577469_1breast cancer 2
SA01577586_1breast cancer 2
SA01577692_1breast cancer 2
SA01577731_1breast cancer 2
SA01577899_1breast cancer 2
SA01577961_1breast cancer 2
SA0157806_1breast cancer 2
SA015781122_1breast cancer 2
SA01578230_1breast cancer 2
SA01578325_1breast cancer 2
SA01578453_1breast cancer 2
SA01578554_1breast cancer 2
SA01578659_1breast cancer 2
SA01578757_1breast cancer 2
SA01578823_1breast cancer 2
SA01578949_1breast cancer 2
SA01579017_1breast cancer 2
SA01579145_1breast cancer 2
SA015792131_1breast cancer 2
SA015793125_1breast cancer 2
SA015794108_1breast cancer 2
SA01579558_1breast cancer 2
SA01579614_1breast cancer 2
SA01579763_1breast cancer 2
SA01579877_1breast cancer 2
SA01579926_1breast cancer 2
SA015800139_1breast cancer 2
SA015801105_1breast cancer 2
SA015802114_1breast cancer 2
SA01580339_1breast cancer 3
SA0158043_1breast cancer 3
SA01580538_1breast cancer 3
SA01580641_1breast cancer 3
SA01580747_1breast cancer 3
SA01580827_1breast cancer 3
SA01580946_1breast cancer 3
SA01581042_1breast cancer 3
SA015811132_1breast cancer 3
SA015812137_1breast cancer 3
SA0158135_1breast cancer 3
SA01581413_1breast cancer 3
SA015815141_1breast cancer 3
SA015816142_1breast cancer 3
SA0158172_1breast cancer 3
SA01581818_1breast cancer 3
SA01581922_1breast cancer 3
SA01582074_1breast cancer 3
SA01582190_1breast cancer 3
SA0158229_1breast cancer 3
SA01582389_1breast cancer 3
SA01582495_1breast cancer 3
SA0158257_1breast cancer 3
SA01582693_1breast cancer 3
SA01582783_1breast cancer 3
SA01582887_1breast cancer 3
SA01582978_1breast cancer 3
SA01583065_1breast cancer 3
SA01583162_1breast cancer 3
SA01583255_1breast cancer 3
SA01583366_1breast cancer 3
SA01583468_1breast cancer 3
SA01583575_1breast cancer 3
SA015836120_1breast cancer 3
SA01583751_1breast cancer 3
SA0158381_1breast cancer 3
SA01583934_1breast cancer 3
SA015840135_1breast cancer 3
SA015841126_1breast cancer 3
SA015842116_1breast cancer 3
SA01584335_1breast cancer 3
SA01584421_1breast cancer 3
SA01584510_1breast cancer 3
SA015846102_1breast cancer 3
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Collection ID:CO000371
Collection Summary:city of hope metabolomics serum profiling data
Sample Type:Blood


Treatment ID:TR000391
Treatment Summary:No treatment done for these samples

Sample Preparation:

Sampleprep ID:SP000384
Sampleprep Summary:A 50 µL aliquot of plasma/serum sample was spiked with two internal standard solutions (10 µl p-chlorophenylalanine in water, 0.1 mg/mL; 10 µL heptadecanoic acid in methanol, 1 mg/mL). The mixed solution was extracted with 175 µL of methanol: chloroform (3:1) and vortexed for 30 seconds. After storing for 10 minutes at –20°C, the samples were centrifuged at 13,000 rpm for 10 minutes. An aliquot of 200 µL supernatant was transferred to a glass sampling vial to vacuum dry at room temperature. The residue was derivatized using a two-step procedure. First, 50 µL methoxyamine (15 mg/mL in pyridine) was added to the vial and kept at 30°C for 90 minutes. After adding 10 µL C10-C40 (all even alkanes, 12.5 µg/mL) as retention index, 50 µL N,O-bis-(trimetylsilyl) trifluoroacetamide (BSTFA) (1% trimethylchlorosilane, TMCS) was added to the samples, before being derivatized at 70°C for 60 minutes. Each 1 µL aliquot of the derivatized solution was injected in splitless mode into an Agilent 6890N gas chromatography coupled with a Pegasus HT time-of-flight mass spectrometry (Leco Co., St. Joseph, MI, USA). To minimize systematic analytical deviations, each control sample was separated by 1 or 2 breast cancer samples. Breast cancer samples from different stages were also run evenly in the whole experiment. Separation was achieved on an Rxi-5 ms capillary column (Crossbond ® 5% diphenyl/95% dimethyl polysiloxane, Restek, PA, USA), with helium as the carrier gas at a constant flow rate of 1.0 mL/min. The temperatures of injection, transfer interface, and ion source were set to 260, 260, and 210°C, respectively. The GC temperature programming was set to 2 min isothermal heating at 80°C, followed by 10°C/min oven temperature ramped to 220°C, 5°C/min to 240°C, and 25°C/min to 290°C, and a final eight minute maintenance at 290°C. Electron impact ionization (70 eV) at full scan mode (m/z 40–600) was used, with an acquisition rate of 20 spectra/second in the TOFMS setting. The data generated in the GC-TOFMS instrument were analyzed by the ChromaTOF software (v4.33, Leco Co, CA, USA). Using the statistic component, the aligned comma separated value (CSV) file can be obtained with sample information, peak information and peak intensity. Peak areas of unique mass were normalized to the internal standard. Compound identification was performed by comparing the mass fragments with NIST 05 Standard mass spectral databases in NIST MS search 2.0 (NIST,Gaithersburg, MD, USA) software with a similarity of more than 70% and reference standards (with retention time, or retention index if available in the library, as another parameter). Internal standards and any known artificial peaks, such as peaks caused by noise, column bleed and BSTFA derivatization procedure, were removed from the dataset before statistical analysis.

Combined analysis:

Analysis ID AN000582 AN000583
Analysis type MS MS
Chromatography type GC Reversed phase
Chromatography system Agilent 6890N Agilent 1200
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um) -
MS instrument type GC x GC-TOF TOF
MS instrument name Leco Pegasus HT TOF Agilent 6220 TOF
Units Peak Intensity Peak Intensity


Chromatography ID:CH000417
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC
Chromatography ID:CH000418
Instrument Name:Agilent 1200
Column Name:-
Chromatography Type:Reversed phase


MS ID:MS000518
Analysis ID:AN000582
Instrument Name:Leco Pegasus HT TOF
Instrument Type:GC x GC-TOF
MS Type:EI
MS ID:MS000519
Analysis ID:AN000583
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF