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MB Sample ID: SA174903
Local Sample ID: | bdivrou_mero_1_met_2 |
Subject ID: | SU001955 |
Subject Type: | Other organism |
Subject Species: | Babesia divergens |
Taxonomy ID: | 32595 |
Genotype Strain: | Rouen 1986 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001955 |
Subject Type: | Other organism |
Subject Species: | Babesia divergens |
Taxonomy ID: | 32595 |
Genotype Strain: | Rouen 1986 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
bdivrou_mero_1_met_2 | SA174903 | FL021497 | Wild-type | Genotype |
Collection:
Collection ID: | CO001948 |
Collection Summary: | Merozoites were isolated from B. divergens infected erythrocite (iRBC) cultures at 40% parasitemia. The content from iRBC culture flasks was transferred to Falcon tubes and spinned at 600 x g and 4 ºC for 5 min. Then, supernatants were filtered once using 5 μm filters and twice using 1.2 μm filters (Versapor membranes) with the help of a 1 mL syringe. Subsequently, the resulting volume was spinned on a Falcon tube at 2000 x g and 4 ºC for 2 min. The supernatants were discarded, and merozoite-containing pellets were placed on ice. |
Sample Type: | merozoites isolated from RBC |
Treatment:
Treatment ID: | TR001967 |
Treatment Summary: | Since this was a qualitative study aiming to characterize specific metabolites from the Babesia divergens merozoites, only one sample group was included and no treatment was performed |
Sample Preparation:
Sampleprep ID: | SP001961 |
Sampleprep Summary: | Metabolite extraction and quenching: four volumes of cold methanol were added to one volume isolated B. divergens merozoite pellets placed on ice and quickly mixed using a high speed vortex. Then, samples were placed in an ice bath for 10 min, Subsequently, samples were transferred to liquid nitrogen for 10 min and thawed in an ice bath for 10 min (this freeze-thaw cycle was repeated two times). Samples were then centrifuged at 5725 x g and 4 ºC for 5 min. Supernatants containing the metabolite extracts were transferred to new tubes, while the remaining pellets were re-extracted twice by adding 400 μL of cold methanol and undergoing the liquid nitrogen freeze-thaw cycles described above. Supernatants obtained for each biological replicate were combined and filtered through 0.22 μm nylon syringe filters and stored at -80 ºC until use. Prior to LC-QqQ/MS analysis, supernatants underwent LC-QqQ/MS-specific sample preparation. First supernatants were thawed on ice and vortex mixed for 2 min. On ice, 300 µL of each supernatant were transferred to LC/MS vials and evaporated using a vacuum concentrator at <10 bar for 2h. The dried extracts were then reconstituted in 60 µL of Milli-Q water with the help of an ultrasonic bath for 5 min. Then, samples were subjected to LC-QqQ/MS analysis. |
Combined analysis:
Analysis ID | AN003081 | AN003082 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
Column | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) |
MS Type | ESI | ESI |
MS instrument type | Triple quadrupole | Triple quadrupole |
MS instrument name | Agilent 6460 QQQ | Agilent 6460 QQQ |
Ion Mode | NEGATIVE | NEGATIVE |
Units |
Chromatography:
Chromatography ID: | CH002253 |
Chromatography Summary: | The chromatographic method consists on a subtle adaptation of the Agilent dMRM method, which uses tributylamine as an ion pairing reagent (for more information, see https://www.agilent.com/cs/library/technicaloverviews/public/5991-6482EN.pdf) |
Instrument Name: | Agilent 1290 Infinity II |
Column Name: | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002827 |
Analysis ID: | AN003081 |
Instrument Name: | Agilent 6460 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | Method 1: Data was acquired in MRM mode. To achieve a higher signal from low-abundance metabolites, transitions corresponding to metabolites of interests were separated in two MS methods (see method 2). Transitions utilized in this study are subtle modifications of the transition dataset contained in the Agilent dMRM database and method (see https://www.agilent.com/cs/library/technicaloverviews/public/5991-6482EN.pdf). Feature assignment was performed by matching transitions and RT with these contained in the Agilent dMRM Database and Method, and further confirmed by addition of authentic MS-grade standards. The software workflow included user visualization in Agilent MassHunter Workstation Software Qualitative Analysis (version B.09.00), and further compound integration using Agilent MassHunter Workstation Software Quantitative Analysis (version B.09.00). Only metabolites with signal-to-noise ratio higher than 3 (limit of detection) were reported. |
Ion Mode: | NEGATIVE |
MS ID: | MS002828 |
Analysis ID: | AN003082 |
Instrument Name: | Agilent 6460 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | Method 1: Data was acquired in MRM mode. To achieve a higher signal from low-abundance metabolites, transitions corresponding to metabolites of interests were separated in two MS methods (see method 2). Transitions utilized in this study are subtle modifications of the transition dataset contained in the Agilent dMRM database and method (see https://www.agilent.com/cs/library/technicaloverviews/public/5991-6482EN.pdf). Feature assignment was performed by matching transitions and RT with these contained in the Agilent dMRM Database and Method, and further confirmed by addition of authentic MS-grade standards. The software workflow included user visualization in Agilent MassHunter Workstation Software Qualitative Analysis (version B.09.00), and further compound integration using Agilent MassHunter Workstation Software Quantitative Analysis (version B.09.00). Only metabolites with signal-to-noise ratio higher than 3 (limit of detection) were reported. |
Ion Mode: | NEGATIVE |