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MB Sample ID: SA315801
| Local Sample ID: | 633 |
| Subject ID: | SU003016 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 22-93 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003016 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 22-93 |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 633 | SA315801 | FL037574 | Septic Shock | Group |
Collection:
| Collection ID: | CO003009 |
| Collection Summary: | Patient samples were selected from the pre-existing Registry of Critical Illness (RoCI) cohort, housed at Brigham and Women’s Hospital (BWH) in Boston, MA, USA. RoCI is approved by the Partners Human Research Committee. Informed consent was obtained for blood collection. Curation of the database identified 21 patients with positive blood cultures growing either Escherichia coli, Klebsiella pneumoniae, or Pseudomonas aeruginosa with contemporaneous or near contemporaneous plasma samples banked and available for metabolomic analysis. Twenty-two controls admitted to the intensive care unit for reasons other than septic shock were identified for use as controls. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003025 |
| Treatment Summary: | No treatment was used in the study |
Sample Preparation:
| Sampleprep ID: | SP003022 |
| Sampleprep Summary: | Plasma samples were thawed on ice and aliquoted to prepare extracts for three different LC-MS methods: HILIC-pos: 10 µL of plasma sample 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 plasma sample 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 plasma sample 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. |
Combined analysis:
| Analysis ID | AN004762 | AN004763 | AN004764 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase |
| Chromatography system | 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 (2.1 mm X 100 mm,1.7 µm,130Å) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | integrated peak area | integrated peak area | integrated peak area |
Chromatography:
| Chromatography ID: | CH003594 |
| 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: | CH003595 |
| 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: | CH003596 |
| 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 (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 |
MS:
| MS ID: | MS004508 |
| Analysis ID: | AN004762 |
| 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: | MS004509 |
| Analysis ID: | AN004763 |
| 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: | MS004510 |
| Analysis ID: | AN004764 |
| 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 |
