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MB Sample ID: SA082900

Local Sample ID:bh-0066
Subject ID:SU001259
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

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Subject:

Subject ID:SU001259
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
bh-0066SA082900FL012575VegetarianDiet

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
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