Return to study ST001057 main page
MB Sample ID: SA071668
Local Sample ID: | PCC 11801_Method 1_Rep5 |
Subject ID: | SU001099 |
Subject Type: | Bacteria |
Subject Species: | Synechococcus |
Taxonomy ID: | 1129 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001099 |
Subject Type: | Bacteria |
Subject Species: | Synechococcus |
Taxonomy ID: | 1129 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
PCC 11801_Method 1_Rep5 | SA071668 | FL011231 | Method 1 | Extraction Method Used |
Collection:
Collection ID: | CO001093 |
Collection Summary: | 20 mL Cyanobacterial cells grown at exponential phase were filtered and extracted with the extraction buffers suggested. |
Sample Type: | Bacterial cells |
Treatment:
Treatment ID: | TR001113 |
Treatment Summary: | Various cells were extracted using the extraction solutions described as Method 1, Method 2A and Method 2B |
Sample Preparation:
Sampleprep ID: | SP001106 |
Sampleprep Summary: | The cell suspension was filtered through a 0.8 µm nylon membrane and the filtered cells was quickly placed in 1.6 ml cold methanol (100%) or methanol-water mixture (80:20 v/v). The mixture was incubated at -80 °C for 1 hour following which the cell-solvent mixture was removed and placed in a 15 mL centrifuge tube. The cells sticking to the filter were then scraped off with chloroform (2.4 mL) and mixed with the cell-solvent mixture. The mixture was vortexed for 20 minutes under cold conditions (vortexed for 30s and kept on ice for 1 minute and the cycle repeated). Two mL of MilliQ water or NH4OH solution in water (at concentrations of 0.2 M, 0.4 M) was added into the mixture to separate the phases. The mixture was vortexed for 10 minutes, centrifuged for 15 minutes at 3200g at 4 °C to obtain two separate phases and the top aqueous-rich layer was collected (approximately 3 mL), evaporated to dryness and stored at -80 °C until further analysis. The stored pellets were reconstituted in 100 μL of 50/50 methanol-water mixture and filtered before injecting on LC/MS. |
Combined analysis:
Analysis ID | AN001726 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Shimadzu 20AD |
Column | Phenomenex Synergi Hydro RP (100 x 2mm,2.5um) |
MS Type | ESI |
MS instrument type | Triple TOF |
MS instrument name | ABI Sciex 5600+ TripleTOF |
Ion Mode | NEGATIVE |
Units | Peak Area |
Chromatography:
Chromatography ID: | CH001220 |
Instrument Name: | Shimadzu 20AD |
Column Name: | Phenomenex Synergi Hydro RP (100 x 2mm,2.5um) |
Flow Rate: | 300 microliter/min |
Solvent A: | 100% water; 10 mM tributylamine |
Solvent B: | 100% methanol |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001596 |
Analysis ID: | AN001726 |
Instrument Name: | ABI Sciex 5600+ TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
Ion Mode: | NEGATIVE |