Summary of Study ST002078

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 PR001318. The data can be accessed directly via it's Project DOI: 10.21228/M8BT55 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 IDST002078
Study TitleMultiple modes of interfering with the activity of Plasmodium falciparum cytoplasmic isoleucyl-tRNA synthetase illustrate the enzyme is a promising antimalarial target.
Study SummaryHere we interrogated the in vitro metabolic effects of 6 drugs using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention. We interrogate the metabolic effects on the 3D7 parasite strain. The metabolic effects were compared to their parent strain. The metabolic fingerprints provided show that certain biochemical pathways are affected by the drug inhibitory effect.
Institute
Pennsylvania State University
DepartmentDepartment of Biochemistry and Molecular Biology
Last NameLlinas
First NameManuel
AddressW126 Millenium Science Complex, University Park, PA 16802
Emailmanuel@psu.edu
Phone814-867-3527
Submit Date2021-12-06
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-10-19
Release Version1
Manuel Llinas Manuel Llinas
https://dx.doi.org/10.21228/M8BT55
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001318
Project DOI:doi: 10.21228/M8BT55
Project Title:Multiple modes of interfering with the activity of Plasmodium falciparum cytoplasmic isoleucyl-tRNA synthetase illustrate the enzyme is a promising antimalarial target.
Project Summary:Here we interrogated the in vitro metabolic effects of 6 drugs using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention. We interrogate the metabolic effects on the 3D7 parasite strain. The metabolic effects were compared to their parent strain. The metabolic fingerprints provided show that certain biochemical pathways are affected by the drug inhibitory effect.
Institute:Pennsylvania State University
Department:Department of Biochemistry and Molecular Biology
Last Name:Llinas
First Name:Manuel
Address:W126 Millenium Science Complex, University Park, PA 16802
Email:manuel@psu.edu
Phone:814-867-3527

Subject:

Subject ID:SU002161
Subject Type:Cultured cells
Subject Species:Plasmodium falciparum
Taxonomy ID:5833
Genotype Strain:3D7

Factors:

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

mb_sample_id local_sample_id Drug
SA196365Blank1Blank
SA196366Blank2Blank
SA196367Blank3Blank
SA196368Halofuginone3Halofuginone
SA196369Halofuginone2Halofuginone
SA196370Halofuginone1Halofuginone
SA196371MMV1081413_1MMV1081413
SA196372MMV1081413_2MMV1081413
SA196373MMV1081413_3MMV1081413
SA196374MMV1091186_2MMV1091186
SA196375MMV1091186_3MMV1091186
SA196376MMV1091186_1MMV1091186
SA196377MMV1578884_1MMV1578884
SA196378MMV1578884_3MMV1578884
SA196379MMV1578884_2MMV1578884
SA196380ND1ND
SA196381ND2ND
SA196382ND3ND
SA196383OSM-S-106-2OSM-S-106
SA196384OSM-S-106-1OSM-S-106
SA196385OSM-S-106-3OSM-S-106
SA196386Pool3Pool
SA196387Pool1Pool
SA196388Pool2Pool
SA196389TCMDC-124553-1TCMDC-124553
SA196390TCMDC-124553-2TCMDC-124553
SA196391TCMDC-124553-3TCMDC-124553
Showing results 1 to 27 of 27

Collection:

Collection ID:CO002154
Collection Summary:Cells were pelleted and the media aspirated prior to extraction
Sample Type:Pf infected RBCs

Treatment:

Treatment ID:TR002173
Treatment Summary:Purified iRBCs were treated with 10XIC50 drug for 2.5 hours

Sample Preparation:

Sampleprep ID:SP002167
Sampleprep Summary:90% Methanol/10% water at 50:1 solvent/cell pellet followed by vortexing and clarification via centrifugation
Processing Method:Lysis
Processing Storage Conditions:4℃
Extraction Method:See SA Cobbold et al JBC 2013
Extract Cleanup:Clarification via centrifugation followed by nitrogen drying
Extract Storage:-80℃
Sample Spiking:Internal Standard 13C4, 15N1-Aspartate used for sample preparation normalizer

Combined analysis:

Analysis ID AN003387 AN003388 AN003389 AN003390
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column Waters XSelect HSS T3 C18 (100 x 2.1mm,2.5um) Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um) Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um) Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode NEGATIVE NEGATIVE NEGATIVE NEGATIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH002503
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters XSelect HSS T3 C18 (100 x 2.1mm,2.5um)
Internal Standard:13C4, 15N1-Aspartate
Preconditioning:Water Blanks
Chromatography Type:Reversed phase
  
Chromatography ID:CH002504
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um)
Internal Standard:13C4, 15N1-Aspartate
Preconditioning:Water Blanks
Chromatography Type:Reversed phase
  
Chromatography ID:CH002505
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um)
Internal Standard:13C4, 15N1-Aspartate
Preconditioning:Water Blanks
Chromatography Type:Reversed phase
  
Chromatography ID:CH002506
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Water XSelect HSS T3 C18 (100 x 2.1mm,2.5um)
Internal Standard:13C4, 15N1-Aspartate
Preconditioning:Water Blanks
Chromatography Type:Reversed phase

MS:

MS ID:MS003154
Analysis ID:AN003387
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:El-Maven was used to process converted .mzXML
Ion Mode:NEGATIVE
  
MS ID:MS003155
Analysis ID:AN003388
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:El-Maven was used to process converted .mzXML
Ion Mode:NEGATIVE
  
MS ID:MS003156
Analysis ID:AN003389
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:El-Maven was used to process converted .mzXML
Ion Mode:NEGATIVE
  
MS ID:MS003157
Analysis ID:AN003390
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:El-Maven was used to process converted .mzXML
Ion Mode:NEGATIVE
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