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MB Sample ID: SA315413
| Local Sample ID: | H-Glu/50_1-pos |
| Subject ID: | SU003003 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Genotype Strain: | BL21(DE3) |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003003 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Genotype Strain: | BL21(DE3) |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| H-Glu/50_1-pos | SA315413 | FL037495 | D-Glycerol | Carbon source |
| H-Glu/50_1-pos | SA315413 | FL037495 | 0 | Percent D2O |
| H-Glu/50_1-pos | SA315413 | FL037495 | positive | MS ionization mode |
Collection:
| Collection ID: | CO002996 |
| Collection Summary: | Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail. |
| Collection Protocol Filename: | Deuterated_Lipids_Methods_Summary.pdf |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR003012 |
| Treatment Summary: | E. coli was grown in Enfors minimal media (deuterated or otherwise) with different carbon sources including glycerol, glucose, D-glycerol, and D-glucose. |
| Cell Media: | Enfors minimal media |
| Cell Harvesting: | 30 mL culture collected by centrifugation at 4k x g |
Sample Preparation:
| Sampleprep ID: | SP003009 |
| Sampleprep Summary: | Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail. |
| Sampleprep Protocol Filename: | Deuterated_Lipids_Methods_Summary.pdf |
| Extraction Method: | Matyash (MTBE) varient |
| Sample Resuspension: | 8:23:69 butanol:isopropanol:water |
Combined analysis:
| Analysis ID | AN004748 | AN004749 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
| Column | In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm. | In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm. |
| MS Type | ESI | ESI |
| MS instrument type | LTQ-FT | LTQ-FT |
| MS instrument name | Thermo Velos Pro Orbitrap | Thermo Velos Pro Orbitrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Presence/Absence | Presence/Absence |
Chromatography:
| Chromatography ID: | CH003581 |
| Chromatography Summary: | Because the columns were packed in-house, there is some variation in the total length (see column description below). |
| Methods Filename: | Deuterated_Lipids_Methods_Summary.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 RS |
| Column Name: | In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm. |
| Column Temperature: | room temp |
| Flow Gradient: | Solvent Gradient: Time (min) 0 1 2.5 7.5 13.5 48.5 58.5 75.5 77.5 87 Solvent A (%) 99 99 70 65 45 30 1 1 99 99 Solvent B (%) 1 1 30 45 55 70 99 99 1 1 |
| Flow Rate: | Split flow nano-chromatography. The actual flow rate at the column is dependent on a variety of factors and an accurate measurement of the flow rate is impractical. The flow rate at the macro pumps were set at either 0.05 or 0.1 mL/min depending on the waste line's backpressure. |
| Solvent A: | 60% acetonitrile/40% water; ~0.4g/L ammonium acetate |
| Solvent B: | 90% sopropanol/10% acetonitrile; ~0.4g/L ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004494 |
| Analysis ID: | AN004748 |
| Instrument Name: | Thermo Velos Pro Orbitrap |
| Instrument Type: | LTQ-FT |
| MS Type: | ESI |
| MS Comments: | Top 10 DDA acquisition: Oribitrap Full-Scan at 30k resolving power from 150-2000 m/z. Data-dependent collisional-induced dissociation (CID) fragmentation scans performed with the LTQ ion trap at 30 normalized collision energy with normal scan rate. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Deuterated_Lipids_Methods_Summary.pdf |
| MS ID: | MS004495 |
| Analysis ID: | AN004749 |
| Instrument Name: | Thermo Velos Pro Orbitrap |
| Instrument Type: | LTQ-FT |
| MS Type: | ESI |
| MS Comments: | Top 10 DDA acquisition: Oribitrap Full-Scan at 30k resolving power from 150-2000 m/z. Data-dependent collisional-induced dissociation (CID) fragmentation scans performed with the LTQ ion trap at 30 normalized collision energy with normal scan rate. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Deuterated_Lipids_Methods_Summary.pdf |
