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MB Sample ID: SA082854
Local Sample ID: | bc-0042 |
Subject ID: | SU001259 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001259 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
bc-0042 | SA082854 | FL012574 | Omnivore | Diet |
Collection:
Collection ID: | CO001253 |
Collection Summary: | Stool samples were obtained from OpenBiome (https://www.openbiome.org/), a non-profit stool bank, under a protocol approved by the institutional review boards at MIT and the Broad Institute (IRB protocol ID #1603506899) |
Sample Type: | Stool |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR001274 |
Treatment Summary: | Subjects were healthy people screened by OpenBiome to minimize the potential for carrying pathogens, with ages between 19-45 years and with BMI between 17.5-29.8 at initial sampling. |
Sample Preparation:
Sampleprep ID: | SP001267 |
Sampleprep Summary: | Raw stool were diluted 1:10 in 12.5% glycerol buffer and 0.9% NaCl, homogenized and filtered through a 330um filter. HILIC-pos: LC-MS samples were prepared from homogenate(10 μL) via protein precipitation with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples are centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were injected directly. HILIC-neg: Stool homogenates (30μL) were extracted using 120 μL of 80% methanol (VWR) containing 0.05 ng/μL inosine-15N4, 0.05 ng/μL thymine-d4, and 0.1 ng/μL glycocholate-d4 as internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000 x g, 4ºC) and the supernatants (10 μL) were injected directly. C18-neg: Stool homogenates (30 μL) were extracted using 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) and centrifuged (10 min, 9,000 x g, 4°C). C8-pos: Lipids were extracted from homogenates (10 μL) using 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000 x g, ambient temperature), supernatants (10 μL) were injected directly |
Combined analysis:
Analysis ID | AN001984 | AN001985 | AN001986 | AN001987 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
Chromatography system | Shimadzu Nexera X2 | Waters Acquity | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
Column | Waters Atlantis HILIC (150 x 2mm) | Phenomenex Luna NH2 (150 x 2mm,3um,100A) | Waters Acquity BEH C18 (150 x 2mm,1.7um) | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Plus Orbitrap |
Ion Mode | POSITIVE | NEGATIVE | NEGATIVE | POSITIVE |
Units | abundance | abundance | Abundance | Abundance |
Chromatography:
Chromatography ID: | CH001432 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Atlantis HILIC (150 x 2mm) |
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: | CH001433 |
Instrument Name: | Waters Acquity |
Column Name: | Phenomenex Luna NH2 (150 x 2mm,3um,100A) |
Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide (Sigma-Aldrich) (VWR) |
Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
Chromatography Type: | HILIC |
Chromatography ID: | CH001434 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity BEH C18 (150 x 2mm,1.7um) |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH001435 |
Instrument Name: | Shimadzu Nexera X2 |
Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
Solvent A: | 95% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate |
Solvent B: | 100% methanol; 0.1% acetic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001837 |
Analysis ID: | AN001984 |
Instrument Name: | Thermo Q Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | 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 or reference samples. |
Ion Mode: | POSITIVE |
MS ID: | MS001838 |
Analysis ID: | AN001985 |
Instrument Name: | Thermo Q Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | 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 or reference samples. |
Ion Mode: | NEGATIVE |
MS ID: | MS001839 |
Analysis ID: | AN001986 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | 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 or reference samples. |
Ion Mode: | NEGATIVE |
MS ID: | MS001840 |
Analysis ID: | AN001987 |
Instrument Name: | Thermo Q Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | 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 or reference samples. |
Ion Mode: | POSITIVE |