Summary of study ST001275

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 IDST001275
Study TitleMetabolomics-based profiling of the mode of action of Pathogen Box compounds in Trypanosoma brucei (part-II)
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

Select appropriate tab below to view additional metadata details:


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:SU001347
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
SA093127DMSO_5DMSO
SA093128DMSO_8DMSO
SA093129DMSO_7DMSO
SA093130DMSO_6DMSO
SA093131MMV099637_4MMV099637
SA093132MMV099637_1MMV099637
SA093133MMV099637_3MMV099637
SA093134MMV099637_2MMV099637
SA093135MMV652003_4MMV652003
SA093136MMV652003_1MMV652003
SA093137MMV652003_3MMV652003
SA093138MMV652003_2MMV652003
SA093139MMV676600_4MMV676600
SA093140MMV676600_3MMV676600
SA093141MMV676600_2MMV676600
SA093142MMV676600_1MMV676600
SA093143MMV676604_4MMV676604
SA093144MMV676604_3MMV676604
SA093145MMV676604_1MMV676604
SA093146MMV676604_2MMV676604
SA093147MMV687706_4MMV687706
SA093148MMV687706_3MMV687706
SA093149MMV687706_1MMV687706
SA093150MMV687706_2MMV687706
SA093151MMV688179_3MMV688179
SA093152MMV688179_4MMV688179
SA093153MMV688179_1MMV688179
SA093154MMV688179_2MMV688179
SA093155MMV688271_4MMV688271
SA093156MMV688271_2MMV688271
SA093157MMV688271_1MMV688271
SA093158MMV688279_4MMV688279
SA093159MMV688279_1MMV688279
SA093160MMV688279_3MMV688279
SA093161MMV688279_2MMV688279
SA093162MMV688467_4MMV688467
SA093163MMV688467_2MMV688467
SA093164MMV688467_3MMV688467
SA093165MMV688467_1MMV688467
SA093166MMV688776_4MMV688776
SA093167MMV688776_3MMV688776
SA093168MMV688776_1MMV688776
SA093169MMV688796_3MMV688796
SA093170MMV688796_1MMV688796
SA093171MMV688796_2MMV688796
SA093172MMV688797_4MMV688797
SA093173MMV688797_2MMV688797
SA093174MMV688797_3MMV688797
SA093175MMV688797_1MMV688797
SA093176MMV688798_4MMV688798
SA093177MMV688798_3MMV688798
SA093178MMV688798_2MMV688798
SA093179MMV688798_1MMV688798
SA093180MMV688958_4MMV688958
SA093181MMV688958_3MMV688958
SA093182MMV688958_1MMV688958
SA093183MMV688958_2MMV688958
SA093184MMV689028_4MMV689028
SA093185MMV689028_3MMV689028
SA093186MMV689028_1MMV689028
SA093187MMV689028_2MMV689028
SA093188MMV689029_3MMV689029
SA093189MMV689029_4MMV689029
SA093190MMV689029_2MMV689029
SA093191MMV689029_1MMV689029
SA093192MMV690027_3MMV690027
SA093193MMV690027_2MMV690027
SA093194MMV690027_1MMV690027
SA093195MMV690028_4MMV690028
SA093196MMV690028_1MMV690028
SA093197MMV690028_2MMV690028
SA093198MMV690028_3MMV690028
Showing results 1 to 72 of 72

Collection:

Collection ID:CO001341
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:TR001362
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:SP001355
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 AN002116
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Ascentis Express C8, 2.7 μm HPLC Column (2.7 μm particle size, L × I.D. 10 cm × 2.1 mm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units Peak height

Chromatography:

Chromatography ID:CH001549
Chromatography Summary:Metabolite extracts were analysed using reversed phase liquid chromatography (LC) and high resolution mass spectrometry on an Orbitrap system.
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Ascentis Express C8, 2.7 μm HPLC Column (2.7 μm particle size, L × I.D. 10 cm × 2.1 mm)
Column Temperature:40°C
Flow Gradient:linear gradient -time, %B as follows: 0min- 0%, 1.5min- 20%, 7min- 28%, 8min- 35%, 24min- 65%, 25min- 100%.
Flow Rate:200 μL/min
Sample Injection:10 μL
Solvent A:40% (v/v) isopropanol, 2 mM formic acid, 8 mM ammonium formate
Solvent B:98% (v/v) isopropanol, 2 mM formic acid, 8 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS001971
Analysis ID:AN002116
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
Spray Voltage:3.5kV
Resolution Setting:70000
Scan Range Moverz:140-1300 m/z
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