Summary of study ST000355

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

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

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Study IDST000355
Study TitleGC/MS and LC/MS metabolomics profiling for breast cancer plasma data and control plasma data
Study Typemetabolomics profiling
Study SummaryUse GC/MS and LC/MS technique to profile breast cancer samples and normal control samples
Institute
University of Hawaii
DepartmentCancer Center
Last NameXie
First NameGuoxiang
Address701 ILALO STREET HONOLULU, HI 96813
Emailgxie@cc.hawaii.edu
Phone(808) 564-5938
Submit Date2016-03-08
Analysis Type DetailGC/LC-MS
Release Date2016-03-16
Release Version1
Guoxiang Xie Guoxiang Xie
https://dx.doi.org/10.21228/M86K6W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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
Address:701 ILALO STREET HONOLULU, HI 96813
Email:gxie@cc.hawaii.edu
Phone:(808) 564-5938

Subject:

Subject ID:SU000376
Subject Type:Human breast cancer and normal controls plasma metabolomics profiling
Subject Species:Homo sapiens
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Diagnosis Stage
SA015536PN02394Breast cancer 1
SA015537PN02307Breast cancer 1
SA015538PN02546Breast cancer 1
SA015539PN02854Breast cancer 1
SA015540PN01935Breast cancer 1
SA015541PN02020Breast cancer 1
SA015542PN02619Breast cancer 1
SA015543PN02261Breast cancer 1
SA015544PN02528Breast cancer 1
SA015545PN02773Breast cancer 1
SA015546PN02453Breast cancer 1
SA015547PN02791Breast cancer 1
SA015548PN02917Breast cancer 1
SA015549PN02760Breast cancer 1
SA015550PN02637Breast cancer 1
SA015551PN02212Breast cancer 1
SA015552PN02956Breast cancer 1
SA015553PN02523Breast cancer 1
SA015554PN02944Breast cancer 1
SA015555PN00737Breast cancer 2
SA015556PN00427Breast cancer 2
SA015557PN00506Breast cancer 2
SA015558PN00465Breast cancer 2
SA015559PN00032Breast cancer 2
SA015560PN00025Breast cancer 2
SA015561PN00746Breast cancer 2
SA015562PN00539Breast cancer 2
SA015563PN00936Breast cancer 2
SA015564PN00527Breast cancer 2
SA015565PN00848Breast cancer 2
SA015566PN02018Breast cancer 2
SA015567PN02021Breast cancer 2
SA015568PN00468Breast cancer 2
SA015569PN00029Breast cancer 2
SA015570PN00693Breast cancer 2
SA015571PN00505Breast cancer 2
SA015572PN00895Breast cancer 2
SA015573PN00443Breast cancer 2
SA015574PN01196Breast cancer 2
SA015575PN00861Breast cancer 2
SA015576PN02118Breast cancer 2
SA015577PN00525Breast cancer 2
SA015578PN02008Breast cancer 2
SA015579PN01342Breast cancer 2
SA015580PN01410Breast cancer 2
SA015581PN00482Breast cancer 2
SA015582PN00373Breast cancer 2
SA015583PN01144Breast cancer 2
SA015584PN00481Breast cancer 2
SA015585PN00272Breast cancer 2
SA015586PN00937Breast cancer 2
SA015587PN00547Breast cancer 2
SA015588PN00919Breast cancer 2
SA015589PN00031Breast cancer 2
SA015590PN02110Breast cancer 2
SA015591PN00537Breast cancer 2
SA015592PN00023Breast cancer 2
SA015593PN00038Breast cancer 2
SA015594PN00743Breast cancer 2
SA015595PN00538Breast cancer 2
SA015596PN01321Breast cancer 2
SA015597PN00414Breast cancer 2
SA015598PN00529Breast cancer 2
SA015599PN00033Breast cancer 2
SA015600PN00515Breast cancer 2
SA015601PN00888Breast cancer 2
SA015602PN01884Breast cancer 2
SA015603PN02304Breast cancer 2
SA015604PN01766-0002.6Breast cancer 3
SA015605PN00377Breast cancer 3
SA015606PN00462Breast cancer 3
SA015607PN01766-0001.5Breast cancer 3
SA015608PN00469Breast cancer 3
SA015609PN00030Breast cancer 3
SA015610PN00271Breast cancer 3
SA015611PN02007Breast cancer 3
SA015612PN00941Breast cancer 3
SA015613PN00733Breast cancer 3
SA015614PN01055-0001Breast cancer 3
SA015615PN00028Breast cancer 3
SA015616PN01055-0002Breast cancer 3
SA015617PN00002Breast cancer 3
SA015618PN01262Breast cancer 3
SA015619PN00437Breast cancer 3
SA015620PN00082Breast cancer 3
SA015621PN01976Breast cancer 3
SA015622PN00333Breast cancer 3
SA015623PN00667Breast cancer 3
SA015624PN01449Breast cancer 3
SA015625PN02249Breast cancer 3
SA015626PN00436Breast cancer 3
SA015627PN00036Breast cancer 3
SA015628PN00614-1Breast cancer 3
SA015629PN02097Breast cancer 3
SA015630PN00751Breast cancer 3
SA015631PN01667Breast cancer 3
SA015632PN01001Breast cancer 3
SA015633PN01932Breast cancer 3
SA015634PN00862Breast cancer 3
SA015635PN00027Breast cancer 3
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Collection:

Collection ID:CO000370
Collection Summary:city of hope metabolomics profiling data
Sample Type:Blood

Treatment:

Treatment ID:TR000390
Treatment Summary:No treatment done for these samples

Sample Preparation:

Sampleprep ID:SP000383
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 AN000580 AN000581
Analysis type MS MS
Chromatography type GC Reversed phase
Chromatography system Agilent 6890N Agilent 1200
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um) -
MS Type EI ESI
MS instrument type GC x GC-TOF TOF
MS instrument name Leco Pegasus HT TOF Agilent 6220 TOF
Ion Mode POSITIVE UNSPECIFIED
Units Peak Intensity Peak Intensity

Chromatography:

Chromatography ID:CH000415
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC
  
Chromatography ID:CH000416
Instrument Name:Agilent 1200
Column Name:-
Chromatography Type:Reversed phase

MS:

MS ID:MS000516
Analysis ID:AN000580
Instrument Name:Leco Pegasus HT TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
  
MS ID:MS000517
Analysis ID:AN000581
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
Ion Mode:UNSPECIFIED
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