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MB Sample ID: SA211114
| Local Sample ID: | H-185 |
| Subject ID: | SU002286 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002286 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| H-185 | SA211114 | FL025979 | T21 | Group |
Collection:
| Collection ID: | CO002279 |
| Collection Summary: | All study participants were enrolled in the Crnic Institute Human Trisome Project (HTP) under a study protocol approved by the Colorado Multiple Institutional Review Board (NCT02864108, see also www.trisome.org). Written informed consent was obtained from all study participants or their legal guardians. Data were generated from deidentified biospecimens and linked to demographics and clinical metadata for analysis. Peripheral blood samples were collected into BD Vacutainer K2 EDTA tubes (BD, Cat # 366643) and processed within 2 hrs of blood draw by centrifugation at 700 x g for 15 min to separate plasma, buffy coat (white blood cells, WBCs), and red blood cells (RBCs) which were aliquoted, flash-frozen, and stored at -80°C. Subsequent processing was carried out as described below, with aliquots selected to minimize freeze/thaw cycles. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002298 |
| Treatment Summary: | n/a |
Sample Preparation:
| Sampleprep ID: | SP002292 |
| Sampleprep Summary: | Metabolite extraction: Samples were thawed on ice and 20 μL of sample was diluted in 480 μL of LC-MS grade cold methanol/acetonitrile/water (5:3:2). Samples were incubated at 4°C for 30 min with vigorous vortexing. Supernatants were clarified by centrifugation (10 min, 18,213 g, 4C) then 50 uL aliquots were transferred to autosampler vials. Lipid extraction: Samples were thawed on ice and 10 uL of sample was diluted in 90 uL of LC-MS grade cold methanol. Samples were briefly vortexed to mix then incubated for 30 min at -20C. Supernatants were clarified by centrifugation (10 min, 18,213 g, 4C) then 25 uL aliquots were transferred to autosampler vials and diluted with 25 uL of 10 mM ammonium acetate. |
Combined analysis:
| Analysis ID | AN003600 | AN003601 | AN003602 | AN003603 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um) | Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | peak area | peak area | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002660 |
| Chromatography Summary: | 5 minute negative metabolites |
| Methods Filename: | Merged_chromatography_methods_metabolites_and_lipids.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002661 |
| Chromatography Summary: | 5 minute positive metabolites |
| Methods Filename: | Merged_chromatography_methods_metabolites_and_lipids.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002662 |
| Chromatography Summary: | 17 minute negative oxylipins |
| Methods Filename: | Merged_chromatography_methods_metabolites_and_lipids.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002663 |
| Chromatography Summary: | 15 minute positive metabolites |
| Methods Filename: | Merged_chromatography_methods_metabolites_and_lipids.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003355 |
| Analysis ID: | AN003600 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003356 |
| Analysis ID: | AN003601 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003357 |
| Analysis ID: | AN003602 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 150-1500 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003358 |
| Analysis ID: | AN003603 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 150-1500 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | POSITIVE |
