Summary of Study ST000356

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	ST000356
Study Title	GC/MS and LC/MS metabolomics profiling for breast cancer serum data and control serum 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
Laboratory	Metabolomics Shared Resource
Last Name	Xie
First Name	Guoxiang
Address	701 ILALO STREET HONOLULU, HI 96813
Email	gxie@cc.hawaii.edu
Phone	(808) 564-5938
Submit Date	2016-03-09
Raw Data File Type(s)	d, raw
Analysis Type Detail	GC-MS/LC-MS
Release Date	2016-03-21
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:	SU000377
Subject Type:	Human breast cancer and normal controls serum metabolomics profiling
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Human

Factors:

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
SA015747	37_1	breast cancer	-
SA015748	123_1	breast cancer	-
SA015749	43_1	breast cancer	-
SA015750	84_1	breast cancer	-
SA015751	50_1	breast cancer	-
SA015752	80_1	breast cancer	-
SA015753	128_1	breast cancer	2
SA015754	117_1	breast cancer	2
SA015755	129_1	breast cancer	2
SA015756	119_1	breast cancer	2
SA015757	136_1	breast cancer	2
SA015758	113_1	breast cancer	2
SA015759	143_1	breast cancer	2
SA015760	140_1	breast cancer	2
SA015761	134_1	breast cancer	2
SA015762	107_1	breast cancer	2
SA015763	98_1	breast cancer	2
SA015764	29_1	breast cancer	2
SA015765	15_1	breast cancer	2
SA015766	104_1	breast cancer	2
SA015767	19_1	breast cancer	2
SA015768	110_1	breast cancer	2
SA015769	11_1	breast cancer	2
SA015770	111_1	breast cancer	2
SA015771	33_1	breast cancer	2
SA015772	81_1	breast cancer	2
SA015773	71_1	breast cancer	2
SA015774	69_1	breast cancer	2
SA015775	86_1	breast cancer	2
SA015776	92_1	breast cancer	2
SA015777	31_1	breast cancer	2
SA015778	99_1	breast cancer	2
SA015779	61_1	breast cancer	2
SA015780	6_1	breast cancer	2
SA015781	122_1	breast cancer	2
SA015782	30_1	breast cancer	2
SA015783	25_1	breast cancer	2
SA015784	53_1	breast cancer	2
SA015785	54_1	breast cancer	2
SA015786	59_1	breast cancer	2
SA015787	57_1	breast cancer	2
SA015788	23_1	breast cancer	2
SA015789	49_1	breast cancer	2
SA015790	17_1	breast cancer	2
SA015791	45_1	breast cancer	2
SA015792	131_1	breast cancer	2
SA015793	125_1	breast cancer	2
SA015794	108_1	breast cancer	2
SA015795	58_1	breast cancer	2
SA015796	14_1	breast cancer	2
SA015797	63_1	breast cancer	2
SA015798	77_1	breast cancer	2
SA015799	26_1	breast cancer	2
SA015800	139_1	breast cancer	2
SA015801	105_1	breast cancer	2
SA015802	114_1	breast cancer	2
SA015803	39_1	breast cancer	3
SA015804	3_1	breast cancer	3
SA015805	38_1	breast cancer	3
SA015806	41_1	breast cancer	3
SA015807	47_1	breast cancer	3
SA015808	27_1	breast cancer	3
SA015809	46_1	breast cancer	3
SA015810	42_1	breast cancer	3
SA015811	132_1	breast cancer	3
SA015812	137_1	breast cancer	3
SA015813	5_1	breast cancer	3
SA015814	13_1	breast cancer	3
SA015815	141_1	breast cancer	3
SA015816	142_1	breast cancer	3
SA015817	2_1	breast cancer	3
SA015818	18_1	breast cancer	3
SA015819	22_1	breast cancer	3
SA015820	74_1	breast cancer	3
SA015821	90_1	breast cancer	3
SA015822	9_1	breast cancer	3
SA015823	89_1	breast cancer	3
SA015824	95_1	breast cancer	3
SA015825	7_1	breast cancer	3
SA015826	93_1	breast cancer	3
SA015827	83_1	breast cancer	3
SA015828	87_1	breast cancer	3
SA015829	78_1	breast cancer	3
SA015830	65_1	breast cancer	3
SA015831	62_1	breast cancer	3
SA015832	55_1	breast cancer	3
SA015833	66_1	breast cancer	3
SA015834	68_1	breast cancer	3
SA015835	75_1	breast cancer	3
SA015836	120_1	breast cancer	3
SA015837	51_1	breast cancer	3
SA015838	1_1	breast cancer	3
SA015839	34_1	breast cancer	3
SA015840	135_1	breast cancer	3
SA015841	126_1	breast cancer	3
SA015842	116_1	breast cancer	3
SA015843	35_1	breast cancer	3
SA015844	21_1	breast cancer	3
SA015845	10_1	breast cancer	3
SA015846	102_1	breast cancer	3

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 134

Collection:

Collection ID:	CO000371
Collection Summary:	city of hope metabolomics serum profiling data
Sample Type:	Blood

Treatment:

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.

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 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:	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:

MS ID:	MS000518
Analysis ID:	AN000582
Instrument Name:	Leco Pegasus HT TOF
Instrument Type:	GC x GC-TOF
MS Type:	EI
Ion Mode:	POSITIVE

MS ID:	MS000519
Analysis ID:	AN000583
Instrument Name:	Agilent 6220 TOF
Instrument Type:	TOF
MS Type:	ESI
Ion Mode:	UNSPECIFIED