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MB Sample ID: SA353520
| Local Sample ID: | MM_27 (adapted) |
| Subject ID: | SU003370 |
| Subject Type: | Bacteria |
| Subject Species: | Mycoplasma mycoides, Minimal cell JCVI-syn3B |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003370 |
| Subject Type: | Bacteria |
| Subject Species: | Mycoplasma mycoides, Minimal cell JCVI-syn3B |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| MM_27 (adapted) | SA353520 | FL041211 | M. mycoides | Sample source |
| MM_27 (adapted) | SA353520 | FL041211 | 27 | Temperature |
| MM_27 (adapted) | SA353520 | FL041211 | - | Time (hrs) |
Collection:
| Collection ID: | CO003363 |
| Collection Summary: | Lipidomics data of M. mycoides and JCVI-syn3B membranes,extracted at different temperatures and time points, represented as molp for each of the samples. Quantification in mol % sample. mol% data were calculated, using pmols of lipid intensities (calculated from intensities of each lipid, measured m/z from the mass spectrometry), standardised to total lipid amount. |
| Collection Protocol Filename: | 240528_TempAdapt_Manuscript_Data.xlsx |
| Sample Type: | Mycoplasma |
Treatment:
| Treatment ID: | TR003379 |
| Treatment Summary: | M. mycodies and JCVI-syn3B cells were grown at different temperatures in 25°C-37°C range and their membranes were extracted at adapted state or at different time points for lipidomic data analysis |
Sample Preparation:
| Sampleprep ID: | SP003377 |
| Sampleprep Summary: | Bacterial samples are harvested at designated time points from the continuous cell culture in the bioreactor system and washed twice at their growth temperature in mycoplasma wash buffer (200 mM NaCl, 25 mM HEPES, 1% glucose, pH 7.0) to remove traces of the growth medium (21000g, 2 min centrifuging steps). Washed cell pellet is resuspended in 150 uL PBS and flash-frozen in liquid nitrogen. Lipids are extracted using a two-step chloroform/methanol procedure (Bligh-Dyer lipid extraction protocol) |
Combined analysis:
| Analysis ID | AN005325 | AN005326 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | None (Direct infusion) | None (Direct infusion) |
| Chromatography system | none | none |
| Column | none | none |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | mol percent | mol percent |
Chromatography:
| Chromatography ID: | CH004028 |
| Instrument Name: | none |
| Column Name: | none |
| Column Temperature: | None |
| Flow Gradient: | None |
| Flow Rate: | None |
| Solvent A: | None |
| Solvent B: | None |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS005055 |
| Analysis ID: | AN005325 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples are analyzed by direct infusion on a QExactive mass spectrometer (Thermo Scientific) equipped with a TriVersa NanoMate ion source (Advion Biosciences). Samples are analyzed in both positive and negative ion modes with a resolution of Rm/z=200=280000 for MS (species structural resolution) and Rm/z=200=17500 for MSMS (subspecies structural resolution) experiments, in a single acquisition. MSMS is triggered by an inclusion list encompassing corresponding MS mass ranges scanned in 1 Da increments. Both MS and MSMS data are combined to monitor CE, DAG and TAG ions as ammonium adducts; cholesterol as ammonium adduct of an acetylated derivative. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005056 |
| Analysis ID: | AN005326 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples are analyzed by direct infusion on a QExactive mass spectrometer (Thermo Scientific) equipped with a TriVersa NanoMate ion source (Advion Biosciences). Samples are analyzed in both positive and negative ion modes with a resolution of Rm/z=200=280000 for MS (species structural resolution) and Rm/z=200=17500 for MSMS (subspecies structural resolution) experiments, in a single acquisition. MSMS is triggered by an inclusion list encompassing corresponding MS mass ranges scanned in 1 Da increments. Both MS and MSMS data are combined to monitor PC, PC O-, as acetate adducts; and CL, PA, PE, PE O-, PG, PI and PS as deprotonated anions. MS only is used to monitor LPA, LPE, LPE O-, LPI and LPS as deprotonated anions; Cer, HexCer, SM, LPC and LPC O- as acetate adducts. |
| Ion Mode: | NEGATIVE |
