Summary of study ST001274

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000860. The data can be accessed directly via it's Project DOI: 10.21228/M8HT2K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001274
Study TitleMetabolomics-based profiling of the mode of action of Pathogen Box compounds in Trypanosoma brucei (part-I)
Study SummaryThe mode of action of anti-Trypanosomal compounds from the Pathogen Box was investigated using an unbiased metabolomics approach. Trypanosoma brucei parasites were incubated for five hours with the test compounds at 0.5 µM concentration. Analysis of cell pellets allowed reproducible detection of diverse metabolites from a range of metabolic pathways.
Institute
Monash University
Last NameCreek
First NameDarren
AddressMonash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Emaildarren.creek@monash.edu
Phone+61 (0) 3 9903 9249
Submit Date2019-11-16
Analysis Type DetailLC-MS
Release Date2020-01-13
Release Version1
Darren Creek Darren Creek
https://dx.doi.org/10.21228/M8HT2K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000860
Project DOI:doi: 10.21228/M8HT2K
Project Title:Metabolomics-based profiling of the mode of action of Pathogen Box compounds in Trypanosoma brucei
Project Summary:The mode of action of anti-Trypanosomal compounds from the Pathogen Box was investigated using an unbiased metabolomics approach. Trypanosoma brucei parasites were incubated for five hours with the test compounds at 0.5 µM concentration. Analysis of cell pellets allowed reproducible detection of diverse metabolites from a range of metabolic pathways.
Institute:Monash University
Last Name:Creek
First Name:Darren
Address:Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
Email:darren.creek@monash.edu
Phone:+61 (0) 3 9903 9249

Subject:

Subject ID:SU001346
Subject Type:Cultured cells
Subject Species:Trypanosoma brucei brucei
Taxonomy ID:5702
Genotype Strain:427

Factors:

Subject type: Cultured cells; Subject species: Trypanosoma brucei brucei (Factor headings shown in green)

mb_sample_id local_sample_id Drug treatment
SA093059DMSO_5DMSO
SA093060DMSO_8DMSO
SA093061DMSO_7DMSO
SA093062DMSO_6DMSO
SA093063MMV099637_4MMV099637
SA093064MMV099637_1MMV099637
SA093065MMV099637_3MMV099637
SA093066MMV099637_2MMV099637
SA093067MMV652003_3MMV652003
SA093068MMV652003_1MMV652003
SA093069MMV652003_2MMV652003
SA093070MMV676600_4MMV676600
SA093071MMV676600_3MMV676600
SA093072MMV676600_1MMV676600
SA093073MMV676600_2MMV676600
SA093074MMV676604_4MMV676604
SA093075MMV676604_2MMV676604
SA093076MMV676604_3MMV676604
SA093077MMV676604_1MMV676604
SA093078MMV687706_4MMV687706
SA093079MMV687706_2MMV687706
SA093080MMV687706_1MMV687706
SA093081MMV687706_3MMV687706
SA093082MMV688179_4MMV688179
SA093083MMV688179_1MMV688179
SA093084MMV688179_3MMV688179
SA093085MMV688271_4MMV688271
SA093086MMV688271_3MMV688271
SA093087MMV688271_2MMV688271
SA093088MMV688279_4MMV688279
SA093089MMV688279_3MMV688279
SA093090MMV688279_1MMV688279
SA093091MMV688467_4MMV688467
SA093092MMV688467_3MMV688467
SA093093MMV688467_1MMV688467
SA093094MMV688776_4MMV688776
SA093095MMV688776_3MMV688776
SA093096MMV688776_1MMV688776
SA093097MMV688776_2MMV688776
SA093098MMV688796_4MMV688796
SA093099MMV688796_1MMV688796
SA093100MMV688796_3MMV688796
SA093101MMV688796_2MMV688796
SA093102MMV688797_4MMV688797
SA093103MMV688797_1MMV688797
SA093104MMV688797_3MMV688797
SA093105MMV688797_2MMV688797
SA093106MMV688798_4MMV688798
SA093107MMV688798_3MMV688798
SA093108MMV688798_2MMV688798
SA093109MMV688798_1MMV688798
SA093110MMV688958_4MMV688958
SA093111MMV688958_1MMV688958
SA093112MMV688958_2MMV688958
SA093113MMV688958_3MMV688958
SA093114MMV689028_3MMV689028
SA093115MMV689028_2MMV689028
SA093116MMV689028_1MMV689028
SA093117MMV689029_4MMV689029
SA093118MMV689029_1MMV689029
SA093119MMV689029_2MMV689029
SA093120MMV690027_4MMV690027
SA093121MMV690027_1MMV690027
SA093122MMV690027_2MMV690027
SA093123MMV690028_4MMV690028
SA093124MMV690028_3MMV690028
SA093125MMV690028_2MMV690028
SA093126MMV690028_1MMV690028
Showing results 1 to 68 of 68

Collection:

Collection ID:CO001340
Collection Summary:Trypanosoma brucei brucei (T.b.b) bloodstream forms (strain 427) were maintained in vitro in 5-10 ml cultures at 37 °C and 5% CO2 in Creeks minimal media supplemented with 10% HMI-9. The cultures were passaged every 2-3 days and cells were grown to a maximum density of 2x106cells/ml.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001361
Treatment Summary:For drug-induced metabolic perturbation experiments, cells were sub-cultured at 10e6cells/ml in 20 ml volume with drugs added at 0.5 µM concentration and incubated for a further 5 hours until cell density reached ~2x10e6cells/ml. Cells were then used for metabolite quenching and extraction.

Sample Preparation:

Sampleprep ID:SP001354
Sampleprep Summary:Metabolism was rapidly quenched by rapidly cooling cultures to 4°C in a dry ice and ethanol bath. Cultures were then centrifuged for 10 minutes at 1250g at 4°C. The supernatant was discarded and cells were washed with 1 ml of cold PBS by centrifugation for 1 minute at 2100g at 4°C. The supernatant was removed and cells were extracted with 100 µl extraction solvent containing chloroform: methanol: water (1:3:1 v/v) followed by vortexing at 4 °C for 1 hour. The resulting suspension was centrifuged for 10 minutes at 2100g at 4°C and the supernatant was transferred to glass vials and stored at -80 °C until analysis by liquid chromatography and high-resolution mass spectrometry.

Combined analysis:

Analysis ID AN002115
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000 RS
Column SeQuant ZIC-pHILIC 5µm polymer (150 x 4.6 mm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units Peak height

Chromatography:

Chromatography ID:CH001548
Chromatography Summary:Metabolite extracts were analysed using hydrophilic interaction (HILIC) liquid chromatography (LC) and high resolution mass spectrometry on an Orbitrap system.
Chromatography Comments:Dionex RSLC3000 UHPLC (Thermo). Column additional info: Merck Sequant ZIC-pHILIC 5 µm polymer metal-free(150 x 4.6 mm)
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:SeQuant ZIC-pHILIC 5µm polymer (150 x 4.6 mm)
Column Temperature:25°C
Flow Gradient:linear gradient -time, %B as follows: 0min- 80%, 15min- 50%, 18min- 5%, 21min- 5%, 24min- 80%, 32min- 80%.
Flow Rate:300 μL/min
Internal Standard:internal standards (CHAPS, CAPS, PIPES and TRIS; all at 1 µM)
Sample Injection:10 μL
Solvent A:20 mM ammonium carbonate in water
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS001970
Analysis ID:AN002115
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The raw LC-MS data was processed using IDEOM.
Ion Mode:UNSPECIFIED
Capillary Temperature:300°C
Capillary Voltage:+50 V
Spray Voltage:4kV
Resolution Setting:35000
Scan Range Moverz:85- 1275 m/z
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