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MB Sample ID: SA014477

Local Sample ID:SA016
Subject ID:SU000337
Subject Type:Bacterial cells
Subject Species:Bacteria
Species Group:Microorganism

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Subject:

Subject ID:SU000337
Subject Type:Bacterial cells
Subject Species:Bacteria
Species Group:Microorganism

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
SA016SA014477FL003282AMedia type

Collection:

Collection ID:CO000331
Collection Summary:-
Sample Type:Spent culture supernatant

Treatment:

Treatment ID:TR000351
Treatment Summary:There are 2 treatments. Each sample is a supernatant from a different bacterial strain grown in culture.There are a total of 17 strains, 10 of which are grown in one type of medium and 7 are grown in another type of medium. Supernatants from the 2 types of media are also submitted for analysis.
Treatment Protocol Filename:StudyDesign_NadirMahmood_072914.pdf

Sample Preparation:

Sampleprep ID:SP000345
Sampleprep Summary:1. After quenching the cells add 1 X 106 dried cells to 1.5 ml eppendorff tube. 2. Place the eppendorf tube with cells on dry ice for 20 minutes or til the cells are completely frozen and ice for 20 minutes, till they are completely thawed. Repeat this step twice. 3. Add 1ml of extraction solvent which has been pre-chilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. to the ependorff tube with cells. 4. Repeat step 2 twice with the extraction solvent. 5. Vortex the sample for 10s and shake for 5min at 4°C using the Orbital Mixing Chilling/Heating plate. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 500µL portions of the supernatant. One for analysis and one for backup. Store one aliquot in the -20°C freezer as a backup. 7. Evaporate one 500µL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. Submit to derivatization.
Sampleprep Protocol Filename:SOP_Extraction_of_Cell_pellets.pdf

Combined analysis:

Analysis ID AN000503 AN000504
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Unspecified Unspecified
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 Peak height Peak height

Chromatography:

Chromatography ID:CH000355
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Unspecified
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
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Isopropanol
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000439
Analysis ID:AN000503
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:120
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Pos
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  
MS ID:MS000440
Analysis ID:AN000504
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:13 l/min
Dry Gas Temp:200
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:325
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
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