Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA254130

Local Sample ID:	CC27
Subject ID:	SU002621
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

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Subject:

Subject ID:	SU002621
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
CC27	SA254130	FL032591	Cervical cancer	Treatment

Collection:

Collection ID:	CO002614
Collection Summary:	Serum samples were collected from two independent tissue banks in South Korea, Dongsan Hospital Human Tissue Bank and Gangnam Severance Hospital Gene Bank. The Severance cohort included 185 samples from ovarian cancer patients, 47 from women with benign ovarian tumor, 50 from invasive cervical cancer and 21 samples from patients with benign uterine tumor. Blood was collected from all patients during surgery after anesthesia and at least 8 hours of fasting. In the Dongsan cohort 88 women had ovarian cancer, 12 had benign ovarian tumor, 10 had benign uterine tumor, and 9 women had cervical cancer. As with the Severance cohort, samples from these patients were collected during surgery after anesthesia and at least 6 hours of fasting. All recruited participants were of Korean descent. Samples from both cohorts were grouped together and patients with ovarian cancer (OC) and all other gynecological malignancies (non-OC) were age matched. The matched cohort included 208 patients with ovarian cancer (mean age 51.9 years) and 137 non-OC patients (mean age 49.9 years). Disease stages and histological characteristics are given in Table 1. Among the OC patients, 93 patients had early stage (I and II) cancer. Ten of the OC patients had recurrent cancer and 9 patients have had their samples collected more than once. In addition to diseased patients, samples from normal controls (women with no known gynecological malignancies) were collected during regular health exams at Severance hospital. In this case, blood was collected at least 8 hours after fasting.
Sample Type:	Blood (serum)

Treatment:

Treatment ID:	TR002633
Treatment Summary:	Serum samples were collected from two independent tissue banks in South Korea, Dongsan Hospital Human Tissue Bank and Gangnam Severance Hospital Gene Bank. The Severance cohort included 185 samples from ovarian cancer patients, 47 from women with benign ovarian tumor, 50 from invasive cervical cancer and 21 samples from patients with benign uterine tumor. Blood was collected from all patients during surgery after anesthesia and at least 8 hours of fasting. In the Dongsan cohort 88 women had ovarian cancer, 12 had benign ovarian tumor, 10 had benign uterine tumor, and 9 women had cervical cancer. As with the Severance cohort, samples from these patients were collected during surgery after anesthesia and at least 6 hours of fasting. All recruited participants were of Korean descent. Samples from both cohorts were grouped together and patients with ovarian cancer (OC) and all other gynecological malignancies (non-OC) were age matched. The matched cohort included 208 patients with ovarian cancer (mean age 51.9 years) and 137 non-OC patients (mean age 49.9 years). Among the OC patients, 93 patients had early stage (I and II) cancer. Ten of the OC patients had recurrent cancer and 9 patients have had their samples collected more than once. In addition to diseased patients, samples from normal controls (women with no known gynecological malignancies) were collected during regular health exams at Severance hospital. In this case, blood was collected at least 8 hours after fasting. As noted earlier, blood from diseased patients was collected after the initiation of anesthesia, and thus could not be directly compared with normal controls without introducing major confounding effects. Therefore, control samples were excluded from our main analysis. However, for information purposes only, we also provide a lipidome comparison between healthy controls and OC patients in supplemental information.

Treatment ID:

TR002633

Treatment Summary:

Serum samples were collected from two independent tissue banks in South Korea, Dongsan Hospital Human Tissue Bank and Gangnam Severance Hospital Gene Bank. The Severance cohort included 185 samples from ovarian cancer patients, 47 from women with benign ovarian tumor, 50 from invasive cervical cancer and 21 samples from patients with benign uterine tumor. Blood was collected from all patients during surgery after anesthesia and at least 8 hours of fasting. In the Dongsan cohort 88 women had ovarian cancer, 12 had benign ovarian tumor, 10 had benign uterine tumor, and 9 women had cervical cancer. As with the Severance cohort, samples from these patients were collected during surgery after anesthesia and at least 6 hours of fasting. All recruited participants were of Korean descent. Samples from both cohorts were grouped together and patients with ovarian cancer (OC) and all other gynecological malignancies (non-OC) were age matched. The matched cohort included 208 patients with ovarian cancer (mean age 51.9 years) and 137 non-OC patients (mean age 49.9 years). Among the OC patients, 93 patients had early stage (I and II) cancer. Ten of the OC patients had recurrent cancer and 9 patients have had their samples collected more than once. In addition to diseased patients, samples from normal controls (women with no known gynecological malignancies) were collected during regular health exams at Severance hospital. In this case, blood was collected at least 8 hours after fasting. As noted earlier, blood from diseased patients was collected after the initiation of anesthesia, and thus could not be directly compared with normal controls without introducing major confounding effects. Therefore, control samples were excluded from our main analysis. However, for information purposes only, we also provide a lipidome comparison between healthy controls and OC patients in supplemental information.

Sample Preparation:

Sampleprep ID:	SP002627
Sampleprep Summary:	Serum samples were thawed on ice, followed by metabolite extraction of the non-polar (lipids) metabolome. Extraction solvent was prepared by adding 725 μL of the isotopically labeled lipid standard mixture to 43.5 mL 2-propanol (1:60 ratio) and was kept on ice. This cold extraction solvent was added to serum samples in a 3:1 ratio (solvent: serum) for protein precipitation followed by vortex mixing for 15 seconds. Samples were centrifuged at 13,000 rpm for 7 minutes and the resulting supernatant was transferred to LC vials. The supernatant was stored at -80 °C until UHPLC-MS analysis, which was performed within one week of preparation. A blank sample, prepared with LC-MS grade water, underwent the same sample preparation process as the serum samples and was analyzed with the rest of the samples. Pooled quality control (QC) samples were prepared by combining 5-10 μL aliquots of the supernatant of each serum sample. This pooled QC sample was analyzed after every 10 LC-MS runs to monitor instrument stability through the course of the experiment. Samples were randomized for sample preparation and were run in a randomized order on consecutive days.

Sampleprep ID:

SP002627

Sampleprep Summary:

Serum samples were thawed on ice, followed by metabolite extraction of the non-polar (lipids) metabolome. Extraction solvent was prepared by adding 725 μL of the isotopically labeled lipid standard mixture to 43.5 mL 2-propanol (1:60 ratio) and was kept on ice. This cold extraction solvent was added to serum samples in a 3:1 ratio (solvent: serum) for protein precipitation followed by vortex mixing for 15 seconds. Samples were centrifuged at 13,000 rpm for 7 minutes and the resulting supernatant was transferred to LC vials. The supernatant was stored at -80 °C until UHPLC-MS analysis, which was performed within one week of preparation. A blank sample, prepared with LC-MS grade water, underwent the same sample preparation process as the serum samples and was analyzed with the rest of the samples. Pooled quality control (QC) samples were prepared by combining 5-10 μL aliquots of the supernatant of each serum sample. This pooled QC sample was analyzed after every 10 LC-MS runs to monitor instrument stability through the course of the experiment. Samples were randomized for sample preparation and were run in a randomized order on consecutive days.

Combined analysis:

Analysis ID	AN004153	AN004154
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Accucore C30 (150 x 2.1mm,2.6um)	Thermo Accucore C30 (150 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap ID-X tribrid	Thermo Orbitrap ID-X tribrid
Ion Mode	NEGATIVE	POSITIVE
Units	chromatographic peak area	chromatographic peak area

Chromatography:

Chromatography ID:	CH003073
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:	50
Flow Gradient:	0-1 min 80-40% A; 1-5 min 40-30% A; 5-5.5 min 30-15% A; 5.5-8 min 15-10% A; 8-8.2 min 10-0% A; 8.2-10.5 0% A; 10.5-10.7 min 0-80% A; 10.7-12.0 min 80% A.
Flow Rate:	0.4 ml min-1
Solvent A:	10 mM ammonium acetate with water/acetonitrile (40:60 v/v)
Solvent B:	10 mM ammonium acetate with 2-isopropanol/acetonitrile (90:10 v/v). 0.1% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH003074
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:	50
Flow Gradient:	0-1 min 80-40% A; 1-5 min 40-30% A; 5-5.5 min 30-15% A; 5.5-8 min 15-10% A; 8-8.2 min 10-0% A; 8.2-10.5 0% A; 10.5-10.7 min 0-80% A; 10.7-12.0 min 80% A.
Flow Rate:	0.4 ml min-1
Solvent A:	10 mM ammonium formate with water/acetonitrile (40:60 v/v) and 0.1% formic acid
Solvent B:	10 mM ammonium formate with 2-isopropanol/acetonitrile (90:10 v/v) and 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003900
Analysis ID:	AN004153
Instrument Name:	Thermo Orbitrap ID-X tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS data were acquired in the 150-2000 m/z range with a 120,000 mass resolution setting. For MS/MS experiments, the Thermo Scientific Deep AcquireX data acquisition workflow was performed. Stepped normalized collision energy (NCE) of 15,30,45 was used for fragmenting precursor ions in the HCD cell followed by Orbitrap analysis at 30,000 mass resolving power. Precursor ions were also fragmented with CID energy of 40 and were analyzed in the ion trap. Data were processed in Compound Discoverer 3.3.
Ion Mode:	NEGATIVE

MS ID:	MS003901
Analysis ID:	AN004154
Instrument Name:	Thermo Orbitrap ID-X tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS data were acquired in the 150-2000 m/z range with a 120,000 mass resolution setting. The most relevant MS parameters and the chromatographic gradient used are given in supplementary section Table S2 and S3, respectively. For MS/MS experiments, the Thermo Scientific Deep AcquireX data acquisition workflow was performed. Stepped normalized collision energy (NCE) of 15,30,45 was used for fragmenting precursor ions in the HCD cell followed by Orbitrap analysis at 30,000 mass resolving power. Precursor ions were also fragmented with CID energy of 40 and were analyzed in the ion trap.
Ion Mode:	POSITIVE