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MB Sample ID: SA247312
| Local Sample ID: | PCC11802 60 SEC SWATH4-1 BR2 |
| Subject ID: | SU002556 |
| Subject Type: | Bacteria |
| Subject Species: | Synechococcus elongatus |
| Taxonomy ID: | 2219813 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002556 |
| Subject Type: | Bacteria |
| Subject Species: | Synechococcus elongatus |
| Taxonomy ID: | 2219813 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| PCC11802 60 SEC SWATH4-1 BR2 | SA247312 | FL031094 | 60 | Time point of 13C labeling (s) |
| PCC11802 60 SEC SWATH4-1 BR2 | SA247312 | FL031094 | SWATH 4 | SWATH Program |
Collection:
| Collection ID: | CO002549 |
| Collection Summary: | Experiments were carried out by growing Synechococcus elongatus PCC 11801 and PCC 11802 cells in shake flask under continuous light conditions. The light intensity was ~300-350 µmole photons m-2 s-1. Twenty mL of culture was collected at OD730 of ~0.5-0.6. Samples were quenched with methanol and extracted using the methanol-chloroform-water method. Extracts were stored at -80°C till LCMS analysis. LCMS analysis was done in the negative ion mode using the SWATH methods. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR002568 |
| Treatment Summary: | The metabolites were extracted using a methanol-chloroform-water method described in the Dynamic 13C-labeling of S.elongatus PCC 11801 and 11802 file of the collection data. |
Sample Preparation:
| Sampleprep ID: | SP002562 |
| Sampleprep Summary: | One aliquot of the metabolite extract of each sample were reconstituted in 100µL 50:50 methanol-water and filtered using nylon syringe filters to remove any particulate matter.The injection volume was 4µL. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004022 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Shimadzu 20AD |
| Column | Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | ABI Sciex 5600+ TripleTOF |
| Ion Mode | NEGATIVE |
| Units | Relative Abundance of Isotopologues |
Chromatography:
| Chromatography ID: | CH002972 |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | The gradient method used is as follows: 0% B (0.01 min), 0% B (2 min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min), 0% B (22 min), and 0% B (30 min) |
| Flow Rate: | 0.3 mL/minute |
| Solvent A: | 100% water; 10 mM tributylamine; 15mM acetic acid |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003769 |
| Analysis ID: | AN004022 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The data was acquired with SWATH methods. The details of SWATH methods can be found in the article https://doi.org/10.1016/j.isci.2020.101704. The quantification of MID of metabolites and fragment ions was performed by integrating the area under the curve of precursor and fragment isotopologues using MultiQuant 3.0.1 (Sciex, Framingham, MA) from the Q1 isolation window of the SWATH program, where all the precursor isotopologues of the respective metabolite were present. The peak areas were used to estimate precursor and product MID: mi=Mi/(∑(j=0)^n Mj ) where mi and Mi represent the normalized relative and unnormalized isotopologue abundance for each precursor/fragment ion in which i 13C atoms are incorporated, and n represents the number of carbon. |
| Ion Mode: | NEGATIVE |
