Summary of Study ST001660

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 PR001065. The data can be accessed directly via it's Project DOI: 10.21228/M81Q3K 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 IDST001660
Study TitlePlasmodium falciparum metabolomics as a result of treatment with putative acetyl-CoA synthetase inhibitors
Study SummaryPlasmodium falciparum cells in culture were treated with respective compounds for 2.5 hours at 10xIC50 values. Metabolites were isolated using 90% methanol, dried, reconstituted in HPLC-grade water, and analyzed by HPLC/MS. Resulting data were analyzed and compiled to generate study data.
Institute
Pennsylvania State University
DepartmentChemistry
LaboratoryLlinás Laboratory
Last NameLlinás
First NameManuel
AddressW126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA
Emailmul27@psu.edu
Phone814-867-3444
Submit Date2021-01-22
Num Groups3
Total Subjects24
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2021-06-01
Release Version1
Manuel Llinás Manuel Llinás
https://dx.doi.org/10.21228/M81Q3K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001065
Project DOI:doi: 10.21228/M81Q3K
Project Title:Plasmodium falciparum metabolomics as a result of treatment with putative acetyl-CoA synthetase inhibitors
Project Summary:Plasmodium falciparum is the most virulent species of parasites that cause malaria. Current drug efforts that are used to combat this deadly disease often employ pharmacologic strategies that inhibit critical parasite metabolic functions. Compounds used in the present study have generated resistance mutations in major acetyl-CoA producing enzymes. Hence, we set out to test the metabolic effects of these compounds on Plasmodium falciparum parasites including those on acetyl-CoA production by treating parasites for 2.5 hours under 10xIC50 of the test compounds. We used a targeted HPLC/mass spectrometry-based approach to analyze parasite metabolism. We find that multiple compounds tested in these studies have led to relative decreases in acetyl-CoA abundance compared to control parasite conditions. These studies are necessary for understanding pharmacology effects on the most virulent human malaria parasite.
Institute:Pennsylvania State University
Department:Chemistry
Laboratory:Llinás Laboratory
Last Name:Llinás
First Name:Manuel
Address:W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA
Email:mul27@psu.edu
Phone:814-867-3444
Funding Source:This work was supported by the Bill and Melinda Gates Foundation (OPP1054480)

Subject:

Subject ID:SU001737
Subject Type:Cultured cells
Subject Species:Plasmodium falciparum
Taxonomy ID:5833
Genotype Strain:3D7
Gender:Not applicable
Cell Counts:1x10^8

Factors:

Subject type: Cultured cells; Subject species: Plasmodium falciparum (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA15202620181008-Blank1Blank
SA15202720181008-Blank2Blank
SA15202820181008-Blank3Blank
SA15202920180815-Blank1Blank
SA15203020180815-Blank3Blank
SA15203120180815-Blank5Blank
SA15203220180815-Blank4Blank
SA15203320181008-Blank4Blank
SA15203420180815-Blank2Blank
SA15203520181008-Blank5Blank
SA15203620171106-Blank2Blank
SA15203720171106-Blank1Blank
SA15203820181220-Blank5Blank
SA15203920171106-Blank3Blank
SA15204020181220-Blank4Blank
SA15204120181220-Blank1Blank
SA15204220181220-Blank2Blank
SA15204320181220-Blank3Blank
SA15204420181008-MMV019721-3MMV019721
SA15204520181008-MMV019721-1MMV019721
SA15204620181008-MMV019721-2MMV019721
SA15204720180815-MMV019721-3MMV019721
SA15204820180815-MMV019721-2MMV019721
SA15204920180815-MMV019721-1MMV019721
SA15205020181220-MMV084978-2MMV084978
SA15205120181220-MMV084978-1MMV084978
SA15205220181220-MMV084978-3MMV084978
SA15205320171106-MMV084978-2MMV084978
SA15205420171106-MMV084978-3MMV084978
SA15205520171106-MMV084978-1MMV084978
SA15205620181220-ND1No treatment
SA15205720180815-ND3No treatment
SA15205820171106-ND3No treatment
SA15205920181220-ND2No treatment
SA15206020171106-ND2No treatment
SA15206120181220-ND3No treatment
SA15206220180815-ND1No treatment
SA15206320180815-ND2No treatment
SA15206420181008-ND3No treatment
SA15206520171106-ND1No treatment
SA15206620181008-ND2No treatment
SA15206720181008-ND1No treatment
SA15206820181220-QC3Pooled Parasite Samples
SA15206920181220-QC1Pooled Parasite Samples
SA15207020181220-QC2Pooled Parasite Samples
SA15207120181008-QC2Pooled Parasite Samples
SA15207220180815-QC3Pooled Parasite Samples
SA15207320180815-QC2Pooled Parasite Samples
SA15207420180815-QC1Pooled Parasite Samples
SA15207520171106-Pool3Pooled Parasite Samples
SA15207620171106-Pool2Pooled Parasite Samples
SA15207720181008-QC3Pooled Parasite Samples
SA15207820181008-QC1Pooled Parasite Samples
SA15207920171106-Pool1Pooled Parasite Samples
Showing results 1 to 54 of 54

Collection:

Collection ID:CO001730
Collection Summary:Plasmodium falciparum 3D7 parasites were cultured in RPMI 1640 medium and magnetically enriched to increase the infected to uninfected RBC ratio. Following hemocytometer counts, 1x10^8 parasites were measured per condition into 5 mL of total media for 2.5 hours in the presence of drug. Medium was aspirated until 1 mL remained on each sample, the sample was transferred to a micro-centrifuge tube, spun, and the medium was aspirated.
Collection Protocol Filename:Metabolite_Extraction_for_LCMS_2017.pdf
Sample Type:Cultured cells
Collection Location:Millenium Science Complex, University Park, Pennsylvania
Storage Conditions:-80℃
Collection Vials:1.5 mL eppendorf
Storage Vials:1.5 mL eppendorf
Collection Tube Temp:On ice
Tissue Cell Quantity Taken:1x10^8 cells per sample in 1 mL total volume

Treatment:

Treatment ID:TR001750
Treatment Summary:Plasmodium falciparum 3D7 parasites were cultured in RPMI 1640 medium and magnetically enriched to increase the infected to uninfected RBC ratio. Following hemocytometer counts, 1x10^8 parasites were measured per condition into 5 mL of total media for 2.5 hours in the presence of drug. No treatment or ND represents control parasites without additional alterations. Compounds (MMV...) are test compounds that were added at 10xIC50 value for the experimental duration. Blanks are sample tubes that follow the same procedures as samples following the quenching of metabolism. Both Pool and QC samples are combined samples of all samples from the analytical batch on that particular day. Dates in YYYYMMDD format are appended to individual samples to indicate the batch in which they were processed.
Treatment Protocol Filename:Metabolite_Extraction_for_LCMS_2017.pdf
Treatment Compound:MMV084978, MMV019721
Treatment Route:Transfer to media by pipette
Treatment Dose:10xIC50
Treatment Dosevolume:5 uL or less
Treatment Doseduration:2.5 hours
Treatment Vehicle:DMSO
Cell Storage:Temperature and gas composition controlled incubator
Cell Growth Container:6-well plate
Cell Growth Config:5 mL in each sample well, 1x10^8 infected red blood cells per well, conditions performed in triplicate
Cell Media:RPMI 1640 containing Albumax, Gentamycin, Hypoxanthine, HEPES, Sodium Bicarbonate

Sample Preparation:

Sampleprep ID:SP001743
Sampleprep Summary:Once samples were obtained, metabolism was quenched with 90% methanol containing 0.25 uM labeled aspartate, cells were centrifuged, and the supernatant was removed by nitrogen drying. Sample was reconstituted in 3% HPLC-grade methanol and run on the instrument.
Processing Method:Wash, spin, quench, spin, dry, store at -80 C until run on the instrument, resuspend
Processing Storage Conditions:On ice
Extraction Method:90% methanol extraction
Extract Cleanup:Centrifugation and nitrogen drying
Sample Resuspension:100 uL 3% methanol with 1 uM chlorpropamide
Sample Spiking:0.25 uM Labeled Aspartate, 1 uM chlorpropamide

Combined analysis:

Analysis ID AN002711
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000
Column Waters XSelect HSS (100 x 2.1mm,2.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode NEGATIVE
Units Normalized and blank subtracted peak area

Chromatography:

Chromatography ID:CH002000
Chromatography Summary:Ion-pairing method using reverse-phase chromatography setup.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XSelect HSS (100 x 2.1mm,2.5um)
Column Temperature:30
Solvent A:97% water/3% methanol; 15 mM acetic acid; 10 mM tributylamine
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS002508
Analysis ID:AN002711
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data was centroided using MSConvert and converted to .mzXML for utilization in MzMine and El-Maven software.
Ion Mode:NEGATIVE
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