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MB Sample ID: SA020309
Local Sample ID: | Inj19_SA21_BruinCSH.d |
Subject ID: | SU000434 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU000434 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Inj19_SA21_BruinCSH.d | SA020309 | FL006506 | 2 Hr | Collection Time |
Collection:
Collection ID: | CO000428 |
Collection Summary: | Liver biopsies were snap frozen in liquid nitrogen and stored at 80. Tissue was pulverized, while frozen and tissue was aliquoted into .6 ml tubes between 30 and 70 mg of liver tissue. 3 replicates are provided per sample. |
Collection Protocol Filename: | StudyDesign_BoteBruinsma_072414.pdf |
Sample Type: | Tissue |
Storage Conditions: | -80 C |
Tissue Cell Quantity Taken: | between 30 and 70 mg |
Treatment:
Treatment ID: | TR000448 |
Treatment Summary: | 2 livers (names 23 and 31) were perfused for 3 hours, providing 4 timecourse (0, 1, 2, 3) biopsies. 3 replicates for each biopsy (A, B ,C). These were the only 2 run on the Lipidomics platform. |
Treatment Protocol Filename: | StudyDesign_BoteBruinsma_072414.pdf |
Sample Preparation:
Sampleprep ID: | SP000441 |
Sampleprep Summary: | 1. Weigh 4mg tissue sample in to a 2mL Eppendorf tube. 2. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. 3. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. 4. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500μL supernatant for analysis, and 500μL for a backup. Store backup aliquots in the -20°C freezer. 5. Evaporate one 500μl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). 6. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 7. Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. 8. Remove supernatant to a new Eppendorf tube. 9. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 10. Submit to derivatization. |
Sampleprep Protocol Filename: | SOP_Extraction_of_Liver_Tissue_Samples.pdf |
Processing Method: | Homogenization |
Combined analysis:
Analysis ID | AN000653 | AN000654 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Agilent 6530 | Agilent 6550 |
Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | QTOF | QTOF |
MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
Ion Mode | POSITIVE | NEGATIVE |
Units | counts | counts |
Chromatography:
Chromatography ID: | CH000471 |
Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
Instrument Name: | Agilent 6530 |
Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
Column Pressure: | 450-850 bar |
Column Temperature: | 65 C |
Flow Gradient: | 15% B to 99%B |
Flow Rate: | 0.6 mL/min |
Internal Standard: | See data dictionary |
Retention Time: | See data dictionary |
Sample Injection: | 1.67 uL |
Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
Analytical Time: | 13 min |
Capillary Voltage: | 3500 V |
Time Program: | 15 min |
Weak Wash Solvent Name: | Isopropanol |
Strong Wash Solvent Name: | Isopropanol |
Target Sample Temperature: | Autosampler temp 4 C |
Randomization Order: | Excel generated |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH000472 |
Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
Instrument Name: | Agilent 6550 |
Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
Column Pressure: | 450-850 bar |
Column Temperature: | 65 C |
Flow Gradient: | 15% B to 99%B |
Flow Rate: | 0.6 mL/min |
Internal Standard: | See data dictionary |
Retention Time: | See data dictionary |
Sample Injection: | 5 uL |
Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
Solvent B: | 90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate |
Analytical Time: | 13 min |
Capillary Voltage: | 3500 V |
Time Program: | 15 min |
Weak Wash Solvent Name: | Isopropanol |
Strong Wash Solvent Name: | Isopropanol |
Target Sample Temperature: | Autosampler temp 4 C |
Randomization Order: | Excel generated |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS000579 |
Analysis ID: | AN000653 |
Instrument Name: | Agilent 6530 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | POSITIVE |
Capillary Voltage: | 3500 V |
Collision Gas: | Nitrogen |
Dry Gas Flow: | 8 L/min |
Dry Gas Temp: | 325 C |
Fragment Voltage: | 120 V |
Fragmentation Method: | Auto MS/MS |
Ion Source Temperature: | 325 C |
Ion Spray Voltage: | 1000 V |
Ionization: | Pos |
Precursor Type: | Intact Molecule |
Reagent Gas: | Nitrogen |
Source Temperature: | 325 C |
Dataformat: | .d |
Desolvation Gas Flow: | 11 L/min |
Desolvation Temperature: | 350 C |
Nebulizer: | 35 psig |
Octpole Voltage: | 750 V |
Resolution Setting: | extended dynamic range |
Scan Range Moverz: | 60-1700 Da |
Scanning Cycle: | 2 Hz |
Scanning Range: | 60-1700 Da |
Skimmer Voltage: | 65 V |
MS ID: | MS000580 |
Analysis ID: | AN000654 |
Instrument Name: | Agilent 6550 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | NEGATIVE |
Capillary Voltage: | 3500 V |
Collision Gas: | Nitrogen |
Dry Gas Flow: | 13 L/min |
Dry Gas Temp: | 200 C |
Fragment Voltage: | 175 V |
Fragmentation Method: | Auto MS/MS |
Ion Source Temperature: | 325 C |
Ion Spray Voltage: | 1000 V |
Ionization: | Neg |
Precursor Type: | Intact Molecule |
Reagent Gas: | Nitrogen |
Source Temperature: | 325 C |
Dataformat: | .d |
Desolvation Gas Flow: | 11 L/min |
Desolvation Temperature: | 350 C |
Nebulizer: | 35 psig |
Octpole Voltage: | 750 V |
Resolution Setting: | extended dynamic range |
Scan Range Moverz: | 60-1700 Da |
Scanning Cycle: | 2 Hz |
Scanning Range: | 60-1700 Da |
Skimmer Voltage: | 65 V |