Summary of Study ST001149

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000768. The data can be accessed directly via it's Project DOI: 10.21228/M8DH49 This work is supported by NIH grant, U2C- DK119886.


Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001149
Study TitlePlasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis
Study TypeDrug Exposure
Study SummaryMetabolic examination/confirmation of resistance mutations and GFP tagging observed in study
Pennsylvania State University
LaboratoryLlinás Laboratory
Last NameLlinás
First NameManuel
AddressW-122 Millennium Science Complex, Pollock Road
Submit Date2019-02-15
Raw Data AvailableYes
Analysis Type DetailLC-MS
Release Date2019-05-15
Release Version1
Manuel Llinás Manuel Llinás application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR000768
Project DOI:doi: 10.21228/M8DH49
Project Title:Plasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis
Project Type:LC-MS Metabolomics
Project Summary:Hydrophilic LC-MS analysis of PfNCR1 Targeting compounds as part of functional validation of publication
Institute:Pennsylvania State University
Laboratory:Llinás Laboratory
Last Name:Llinás
First Name:Manuel
Address:W-122 Millennium Science Complex, Pollock Road, University Park, PA 16802
Phone:Office: (814) 867-3444, Lab: (814) 867-3527
Publications:Plasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis
Contributors:Eva S. Istvan, Sudipta Das, Suyash Bhatnagar, Josh R. Beck, Edward Owen, Manuel Llinás, Suresh M. Ganesan, Jacquin C. Niles, Elizabeth A. Winzeler, Akhil B. Vaidya, Daniel E. Goldberg


Subject ID:SU001214
Subject Type:Cultured cells
Subject Species:Plasmodium falciparum
Taxonomy ID:5833


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

mb_sample_id local_sample_id Drug treatment
SA079821ATQ-20180530Atovaquone, 2.5 hours
SA079822ATQ-MB2Atovaquone, 2.5 hours
SA079823ATQ-MB1Atovaquone, 2.5 hours
SA079824ATQ-20181025Atovaquone, 2.5 hours
SA079825MMV009108-MB2MMV009108, 2.5 hours
SA079826MMV009108-20180530MMV009108, 2.5 hours
SA079827MMV019662-MB1MMV019662, 2.5 hours
SA079828MMV019662-20180530MMV019662, 2.5 hours
SA079829MMV028038-20180530MMV028038, 2.5 hours
SA079830MMV028038-20181025MMV028038, 2.5 hours
SA079831ND-MB2Untreated, 2.5 hours
SA079832ND-20181025Untreated, 2.5 hours
SA079833ND-20180530Untreated, 2.5 hours
SA079834ND-MB1Untreated, 2.5 hours
Showing results 1 to 14 of 14


Collection ID:CO001208
Collection Summary:Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes, centrifugation, removal of supernatant, PBS wash, centrifugation, and extraction via 90% methanol with labelled aspartate.
Collection Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Sample Type:Cultured cells
Collection Method:Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes
Collection Location:Biological safety hood
Collection Frequency:once after 2.5 hours treatment
Collection Duration:Collection and extraction occurs in under 20 minutes per plate
Volumeoramount Collected:1 mL containing 1x10^8 infected cells
Storage Conditions:On ice
Collection Vials:1.5 mL eppendorf
Storage Vials:1.5 mL eppendorf


Treatment ID:TR001229
Treatment Summary:Infected Red Blood cells were exposed to Antimalarial Compounds, associated with sample names. All samples were treated with 10xIC50 of a compound for 2.5 hours or left untreated for 2.5 hours.
Treatment Protocol ID:Metabolite_Extraction_for_LCMS_2017_Llinas
Treatment Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Treatment Compound:ATQ, MMV009108, MMV019662, MMV028038
Treatment Route:Addition to media
Treatment Dose:10xIC50, 2-10xIC50 for archival data
Treatment Dosevolume:Always equal to or less than 10 uL per 5 mL sample
Treatment Doseduration:2.5 hours
Treatment Vehicle:Stocks kept in either DMSO or Water
Cell Storage:Temperature/Gas Mixture controlled incubator
Cell Growth Container:6-well plate
Cell Growth Config:5 mL per well, each with 1x10^8 cells
Cell Media:RPMI 1640 w/ Albumax, Gentamycin, Hypoxanthine, HEPES, Sodium Bicarbonate
Cell Harvesting:PBS Wash followed by 90% methanol extraction

Sample Preparation:

Sampleprep ID:SP001222
Sampleprep Summary:Samples washed in PBS, spun down, aspirated, extracted in 90% methanol with labelled aspartate, then dried, resuspended in water labelled with chlorpropamide
Sampleprep Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Processing Method:Wash, Lysis, Drying, resuspension
Processing Storage Conditions:On ice
Extraction Method:90% Methanol Lysis
Extract Storage:-80℃
Sample Resuspension:100 uL water with chlorpropamide
Sample Spiking:Labelled Aspartate, Chlorpropamide

Combined analysis:

Analysis ID AN001896
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000
Column Waters XSelect HSS T3 XP (100 x 2.1mm,2.5um)
MS instrument type Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap
Units Peak Area Post-Blank Subtraction


Chromatography ID:CH001373
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XSelect HSS T3 XP (100 x 2.1mm,2.5um)
Chromatography Type:Reversed phase


MS ID:MS001752
Analysis ID:AN001896
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Blank subtraction, RSD cutoffs both by RSD per sample and pooled QCs to eliminate metabolites affected by time-dependency