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MB Sample ID: SA254994
| Local Sample ID: | HC011_N |
| Subject ID: | SU002636 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002636 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| HC011_N | SA254994 | FL032654 | normal | Tissue type |
Collection:
| Collection ID: | CO002629 |
| Collection Summary: | HCC and normal samples were collected surgically and stored as part of the Mass General Brigham Institutional Review Board (protocol number 2008P001466). Frozen tissue was accessed to create the cohort used in this study. |
| Collection Protocol ID: | MGB IRB 2008P001466 |
| Sample Type: | Oncocytic (Hürthle cell) thyroid carcinoma (HCC) tumors and normal thyroid tissue |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002648 |
| Treatment Summary: | no treatment was used in the study |
Sample Preparation:
| Sampleprep ID: | SP002642 |
| Sampleprep Summary: | Frozen tissues were weighed and homogenized in 4 volumes of water (4 µL of water/mg tissue, 4°C) using a bead beater (TissueLyser II, QIAGEN; Germantown, MD). Tissue homogenates were aliquoted to prepare extracts for four different LC-MS methods: HILIC-pos: 10 µL of each tissue homogenate was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each tissue homogenate was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C8-pos: 10 µL of each tissue homogenate was extracted using 190 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL). The samples were centrifuged (10 min, 9,000 x g, ambient temperature), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C18-neg: 30 µL of each tissue homogenate was extracted using 90 µL of methanol containing 15R-15-methyl PGA2, 15S-15-methyl PGD2, 15S-15-methyl PGE1, 15S-15-methyl PGE2, and 15R-15-methyl PGF2alpha as an internal standards (Cayman Chemical Co.; Ann Arbor, MI). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. |
Combined analysis:
| Analysis ID | AN004171 | AN004172 | AN004173 | AN004174 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2.1mm,3um,100Å | Phenomenex Luna NH2 (150 x 2 mm,5um;100Å) | Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å) | Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | peak area | peak area | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003089 |
| Chromatography Summary: | HILIC-pos: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the positive ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2.1mm,3um,100Å |
| Column Temperature: | 30 |
| Flow Gradient: | 0-0.5 min, isocratic 95% B; 0.5-10.5 min, gradient to 40% B; 10.5-15 min, isocratic 40% B; 15-17 min, gradient to 95% B |
| Flow Rate: | 250 uL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003090 |
| Chromatography Summary: | HILIC-neg: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the negative ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna NH2 (150 x 2 mm,5um;100Å) |
| Column Temperature: | 30 |
| Flow Gradient: | 0-10 min, gradient from 90% B to 0% B; 10-12 min, isocratic 0% B; 12-14 min, gradient from 0% B to 90% B |
| Flow Rate: | 400 uL/min |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% methanol/25% acetonitrile; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003091 |
| Chromatography Summary: | C8-pos: Reversed-phase C8 chromatography analysis of polar and nonpolar lipids in the positive ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-1 min, isocratic 20% B; 1-3 min, gradient to 80% B; 3-10 min, gradient to 100% B; 10-13 min, isocratic 100% B; 13-14 min, gradient to 20% B |
| Flow Rate: | 450 uL/min |
| Solvent A: | 95% water/5% methanol; 0.1% formic acid; 10 mM ammonium acetate |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003092 |
| Chromatography Summary: | C18-neg: Reversed-phase C18 chromatography analysis of compounds of intermediate polarity in the negative ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-3 min, isocratic 20% B; 3-15 min, gradient to 100% B; 15-18 min, isocratic 100% B; 18-19 min, gradient to 20% B |
| Flow Rate: | 450 uL/min |
| Solvent A: | 100% water; 0.01% formic acid |
| Solvent B: | 100% acetonitrile; 0.01% acetic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003918 |
| Analysis ID: | AN004171 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 70-800 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 40, sweep gas 2, spray voltage 3.5 kV, capillary temperature 350°C, S-lens RF 40, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 250 ms. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003919 |
| Analysis ID: | AN004172 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-750 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.0 kV; capillary temperature, 350°C; probe heater temperature, 325 °C; sheath gas, 55; auxiliary gas, 10; and S-lens RF level 50. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003920 |
| Analysis ID: | AN004173 |
| Instrument Name: | Thermo Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 200–1100 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 50, in source CID 5 eV, sweep gas 5, spray voltage 3 kV, capillary temperature 300°C, S-lens RF 60, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 100 ms. Representative standards from each lipid class were used to identify lipids based on RT and m/z patterns, and characteristic product ion spectra. Lipid identities were denoted by total acyl carbon number and total number of double bond number. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003921 |
| Analysis ID: | AN004174 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-850 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.5 kV; capillary temperature, 320°C; probe heater temperature, 300 °C; sheath gas, 45; auxiliary gas, 10; and S-lens RF level 60. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards. |
| Ion Mode: | NEGATIVE |
