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MB Sample ID: SA215693

Local Sample ID:9882
Subject ID:SU002333
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

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Subject:

Subject ID:SU002333
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
9882SA215693FL0260452 monthshost_age

Collection:

Collection ID:CO002326
Collection Summary:Fecal samples were collected at birth (between 0 and 10 days post-delivery, median = 1 day, time point labeled as “birth”), during subsequent scheduled visits, and when possible during illness episodes. Stool samples were initially stored at -20°C at the International Centre for Diarrhoeal Disease Research (Bangladesh) and subsequently transferred to -80°C for shipment on dry ice to Nestlé Research where they were stored at -80°C until analysis.
Sample Type:Feces

Treatment:

Treatment ID:TR002345
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002339
Sampleprep Summary:Stool samples were homogenized in 10 μL of water per milligram stool sample weight using a bead mill (TissueLyser II; Qiagen) and the aqueous homogenates were aliquoted for metabolite profiling analyses. LC-MS samples were prepared for four profiling methods as follows: HILIC-pos: Metabolites were extracted by adding 90 μL 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) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis.

Combined analysis:

Analysis ID AN003670 AN003671 AN003672 AN003673
Analysis type MS MS MS MS
Chromatography type HILIC Reversed phase HILIC Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2mm,3um) Waters Acquity BEH C8 (100 x 2.1mm,1.7um) Phenomenex Luna NH2 (150 x 2.1mm,3um) Waters Acquity T3 (150 x 2.1 mm,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 Plus Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units Abundances Abundances Unitless Abundances Abundances

Chromatography:

Chromatography ID:CH002720
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2mm,3um)
Chromatography Type:HILIC
  
Chromatography ID:CH002721
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002722
Instrument Name:Shimadzu Nexera X2
Column Name:Phenomenex Luna NH2 (150 x 2.1mm,3um)
Chromatography Type:HILIC
  
Chromatography ID:CH002723
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity T3 (150 x 2.1 mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003421
Analysis ID:AN003670
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:MS003422
Analysis ID:AN003671
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:MS003423
Analysis ID:AN003672
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:MS003424
Analysis ID:AN003673
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
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