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

Study ID	ST000355
Study Title	GC/MS and LC/MS metabolomics profiling for breast cancer plasma data and control plasma data
Study Type	metabolomics profiling
Study Summary	Use GC/MS and LC/MS technique to profile breast cancer samples and normal control samples
Institute	University of Hawaii
Department	Cancer Center
Last Name	Xie
First Name	Guoxiang
Address	701 ILALO STREET HONOLULU, HI 96813
Email	gxie@cc.hawaii.edu
Phone	(808) 564-5938
Submit Date	2016-03-08
Raw Data File Type(s)	d, raw
Analysis Type Detail	GC-MS/LC-MS
Release Date	2016-03-16
Release Version	1

Select appropriate tab below to view additional metadata details:

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
Taxonomy ID:	9606
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
SA015536	PN02394	Breast cancer	1
SA015537	PN02307	Breast cancer	1
SA015538	PN02546	Breast cancer	1
SA015539	PN02854	Breast cancer	1
SA015540	PN01935	Breast cancer	1
SA015541	PN02020	Breast cancer	1
SA015542	PN02619	Breast cancer	1
SA015543	PN02261	Breast cancer	1
SA015544	PN02528	Breast cancer	1
SA015545	PN02773	Breast cancer	1
SA015546	PN02453	Breast cancer	1
SA015547	PN02791	Breast cancer	1
SA015548	PN02917	Breast cancer	1
SA015549	PN02760	Breast cancer	1
SA015550	PN02637	Breast cancer	1
SA015551	PN02212	Breast cancer	1
SA015552	PN02956	Breast cancer	1
SA015553	PN02523	Breast cancer	1
SA015554	PN02944	Breast cancer	1
SA015555	PN00737	Breast cancer	2
SA015556	PN00427	Breast cancer	2
SA015557	PN00506	Breast cancer	2
SA015558	PN00465	Breast cancer	2
SA015559	PN00032	Breast cancer	2
SA015560	PN00025	Breast cancer	2
SA015561	PN00746	Breast cancer	2
SA015562	PN00539	Breast cancer	2
SA015563	PN00936	Breast cancer	2
SA015564	PN00527	Breast cancer	2
SA015565	PN00848	Breast cancer	2
SA015566	PN02018	Breast cancer	2
SA015567	PN02021	Breast cancer	2
SA015568	PN00468	Breast cancer	2
SA015569	PN00029	Breast cancer	2
SA015570	PN00693	Breast cancer	2
SA015571	PN00505	Breast cancer	2
SA015572	PN00895	Breast cancer	2
SA015573	PN00443	Breast cancer	2
SA015574	PN01196	Breast cancer	2
SA015575	PN00861	Breast cancer	2
SA015576	PN02118	Breast cancer	2
SA015577	PN00525	Breast cancer	2
SA015578	PN02008	Breast cancer	2
SA015579	PN01342	Breast cancer	2
SA015580	PN01410	Breast cancer	2
SA015581	PN00482	Breast cancer	2
SA015582	PN00373	Breast cancer	2
SA015583	PN01144	Breast cancer	2
SA015584	PN00481	Breast cancer	2
SA015585	PN00272	Breast cancer	2
SA015586	PN00937	Breast cancer	2
SA015587	PN00547	Breast cancer	2
SA015588	PN00919	Breast cancer	2
SA015589	PN00031	Breast cancer	2
SA015590	PN02110	Breast cancer	2
SA015591	PN00537	Breast cancer	2
SA015592	PN00023	Breast cancer	2
SA015593	PN00038	Breast cancer	2
SA015594	PN00743	Breast cancer	2
SA015595	PN00538	Breast cancer	2
SA015596	PN01321	Breast cancer	2
SA015597	PN00414	Breast cancer	2
SA015598	PN00529	Breast cancer	2
SA015599	PN00033	Breast cancer	2
SA015600	PN00515	Breast cancer	2
SA015601	PN00888	Breast cancer	2
SA015602	PN01884	Breast cancer	2
SA015603	PN02304	Breast cancer	2
SA015604	PN01766-0002.6	Breast cancer	3
SA015605	PN00377	Breast cancer	3
SA015606	PN00462	Breast cancer	3
SA015607	PN01766-0001.5	Breast cancer	3
SA015608	PN00469	Breast cancer	3
SA015609	PN00030	Breast cancer	3
SA015610	PN00271	Breast cancer	3
SA015611	PN02007	Breast cancer	3
SA015612	PN00941	Breast cancer	3
SA015613	PN00733	Breast cancer	3
SA015614	PN01055-0001	Breast cancer	3
SA015615	PN00028	Breast cancer	3
SA015616	PN01055-0002	Breast cancer	3
SA015617	PN00002	Breast cancer	3
SA015618	PN01262	Breast cancer	3
SA015619	PN00437	Breast cancer	3
SA015620	PN00082	Breast cancer	3
SA015621	PN01976	Breast cancer	3
SA015622	PN00333	Breast cancer	3
SA015623	PN00667	Breast cancer	3
SA015624	PN01449	Breast cancer	3
SA015625	PN02249	Breast cancer	3
SA015626	PN00436	Breast cancer	3
SA015627	PN00036	Breast cancer	3
SA015628	PN00614-1	Breast cancer	3
SA015629	PN02097	Breast cancer	3
SA015630	PN00751	Breast cancer	3
SA015631	PN01667	Breast cancer	3
SA015632	PN01001	Breast cancer	3
SA015633	PN01932	Breast cancer	3
SA015634	PN00862	Breast cancer	3
SA015635	PN00027	Breast 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.

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 (30m 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 (30m 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