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MB Sample ID: SA006221
| Local Sample ID: | 041113_SentericaCells_RidAKO_Pool_MSMS_0070 |
| Subject ID: | SU000138 |
| Subject Type: | Bacterial cells |
| Subject Species: | Salmonella enterica;Escherichia coli |
| Taxonomy ID: | 28901|562 |
| Genotype Strain: | DM14100|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2|K 12 MG1655|K 12 MG1655 ridA3::tn10 ΔyoaB624::cat STM1549-26::kan| | |yjeF::kan |
| Species Group: | Microorganism |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000138 |
| Subject Type: | Bacterial cells |
| Subject Species: | Salmonella enterica;Escherichia coli |
| Taxonomy ID: | 28901|562 |
| Genotype Strain: | DM14100|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2|K 12 MG1655|K 12 MG1655 ridA3::tn10 ΔyoaB624::cat STM1549-26::kan| | |yjeF::kan |
| Species Group: | Microorganism |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 041113_SentericaCells_RidAKO_Pool_MSMS_0070 | SA006221 | FL001595 | S.enterica | Strain |
| 041113_SentericaCells_RidAKO_Pool_MSMS_0070 | SA006221 | FL001595 | RidA Knock-out | genotype |
Collection:
| Collection ID: | CO000122 |
| Collection Summary: | - |
| Sample Type: | Bacterial Cells |
| Collection Method: | 6 independent colonies of each cell line were grown in M9 minimal medium at 37C until OD600 reached 1.5-2.0. An equivalent of 1 mL at OD 2.0 was placed into a 1.5 mL Eppi tube and spun for 15 sec. After removal of a 0.5 mL medium aliquot, remaining medium was removed and cell pellet was frozen in liquid nitrogen. |
| Collection Location: | University of Florida, Gainesville |
| Collection Vials: | 1.5 mL eppendorf tube |
| Storage Vials: | 1.5 mL eppendorf tube |
Treatment:
| Treatment ID: | TR000140 |
Sample Preparation:
| Sampleprep ID: | SP000135 |
| Sampleprep Summary: | - |
| Processing Storage Conditions: | on ice |
| Extraction Method: | 1.1 mL of cold, degassed extraction solvent (3:1 Methanol:Water) was added to each sample. Samples were vortexed for 20 sec then placed in sonicator for 5 min, followed by another 20 sec vortex. Samples were placed in -20C for 30 minutes prior to spinning down in centrifuge at 14 rcf for 5 min. The supernatant was transferred to 1.5 mL eppendorf tubes and evaporated in the Labconco speed vac. |
| Extract Storage: | -80C |
| Sample Resuspension: | H20 + 5mM NH4OAc + 0.2% Acetic Acid |
Combined analysis:
| Analysis ID | AN000200 | AN000201 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Agilent 1290 | Agilent 1290 |
| Column | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6530 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000133 |
| Chromatography Summary: | Untargeted LC MS |
| Instrument Name: | Agilent 1290 |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Pressure: | 300 bar (max) |
| Column Temperature: | 40 C |
| Flow Gradient: | 0 - 4 min: 0% B; 4-12 min: linear gradient to 45% B; 12-20 min: 45% B |
| Flow Rate: | 0.25 mL/min |
| Injection Temperature: | 4C |
| Sample Injection: | 5 uL |
| Solvent A: | 100% water; 0.2% acetic acid; 5mM ammonium acetate |
| Solvent B: | 90% acetonitrile/10% water; 0.2% acetic acid; 5 mM ammonium acetate |
| Oven Temperature: | H20 + 5mM NH4OAc + 0.2% Acetic Acid |
| Time Program: | 20 min |
| Weak Wash Solvent Name: | 50:50 Methanol:Water |
| Weak Wash Volume: | 15 seconds |
| Target Sample Temperature: | Autosampler temperature 4C |
| Randomization Order: | Excel generated |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000163 |
| Analysis ID: | AN000200 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3000 |
| Collision Energy: | Ramped 0.02eV/m/z + 10 eV |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | Nebulizer: 10 L/min Sheath: 9 L/min |
| Dry Gas Temp: | Nebulizer and Sheath: 350 |
| Fragment Voltage: | 125 |
| Ionization: | Positive |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Dataformat: | .d |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 100 - 1700 m/z |
| Scanning Cycle: | 2 |
| MS ID: | MS000164 |
| Analysis ID: | AN000201 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3000 |
| Collision Energy: | Ramped 0.02eV/m/z + 10 eV |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | Nebulizer: 10 L/min Sheath: 9 L/min |
| Dry Gas Temp: | Nebulizer and Sheath: 350 |
| Fragment Voltage: | 125 |
| Ionization: | Negative |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Dataformat: | .d |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 100 - 1700 m/z |
| Scanning Cycle: | 2 |
