Summary of Study ST000578

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 PR000384. The data can be accessed directly via it's Project DOI: 10.21228/M8DP41 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 IDST000578
Study TitleExperiment HuA: Metabolomics of plasma samples from humans infected with Plasmodium vivax strain.
Study TypeLongitudinal study and treatment of multiple individuals with Chloroquine
Study SummaryPatients with vivax malaria were enrolled in this study from June 2011 to December 2012 at the Fundacão de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), an infectious disease referral center located in Manaus, Western Brazilian Amazon. This study, which required a 42-day follow-up period, was approved by the FMT-HVD Institutional Review Board and the Brazilian National Ethics Committee (CONEP) (IRB approval #: CAAE: 12516713.8.0000.0005). All protocols and documentation were reviewed and sample shipments approved by the Emory IRB. Male and female patients were eligible for inclusion if aged 6 months to 60 years, bodyweight >=5 kg, presenting a blood parasite density from 250 to 100,000 parasites/microliter and axillary temperature >=37.5°C or history of fever in the last 48 hours. Exclusion criteria were: use of antimalarials in the previous 30 days, refusal to be followed up for 42 days and any clinical complication. Patients received supervised treatment with 25 mg/kg of chloroquine (CQ) phosphate over a 3-day period (10 mg/kg on day 0 and 7.5 mg/kg on days 1 and 2). Primaquine (0.5 mg/kg per day for 7 days) was prescribed at the end of the 42-day follow-up period. Patients who vomited the first dose within 30 minutes after drug ingestion were re-treated with the same dose. Patients were evaluated on days 0, 1, 2, 3, 7, 14, 28 and 42 and, if they felt ill, at any time during the study period. Blood smear readings, complete blood counts, and diagnostic polymerase chain reaction (PCR) amplifications were performed at all time points. Three aliquots of 100 µL of whole blood from the day of a recurrence were spotted onto filter paper for later analysis by high performance liquid chromatography (HPLC) to estimate the levels of CQ and desethylchloroquine (DCQ) as previously described. In this study, CQ-resistance with parasitological failure was defined as parasite recurrence in the presence of plasma concentrations of CQ and DSQ higher than 100 ng/mL and microsatellite analysis revealing the presence of the same clonal nature at diagnosis and recurrence. The CQ-sensitive control group consisted of patients with no parasitemia recurring during follow-up period. A group of 20 healthy individuals from Brazil was used as non-malarial control group. Within the MaHPIC, this project is known as ‘Experiment HuA’. This dataset was produced by Dean Jones at Emory University.
Institute
Emory University
DepartmentSchool of Medicine, Vaccine Center at Yerkes
Last NameGalinksi
First NameMary
AddressEmory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
Emailmahpic@emory.edu
PhoneNone
Submit Date2017-02-20
Num Groups273
Total Subjects220
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-07-10
Release Version1
Mary Galinksi Mary Galinksi
https://dx.doi.org/10.21228/M8DP41
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000384
Project DOI:doi: 10.21228/M8DP41
Project Title:The Malaria Host-Pathogen Interaction Center (MaHPIC)
Project Type:Systems Biology
Project Summary:The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program supported by an NIH/NIAID contract (# HHSN272201200031C; see http://www.systemsbiology.emory.edu/index.html). The MaHPIC generates many data types (e.g., metabolomics, functional genomics, lipidomics, proteomics, clinical, parasitological, immune response) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates, and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC: Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director), and Ebru Karpuzoglu ekarpuzoglu@emory.edu (MaHPIC Scientific Project Manager)
Institute:Emory University
Department:School of Medicine, Vaccine Center at Yerkes
Last Name:Galinski
First Name:Mary
Address:Emory University, 954 Gatewood Rd, Atlanta, GA 30329
Email:mgalins@emory.edu
Phone:N/A
Funding Source:NIAID Contract: # HHSN272201200031C

Subject:

Subject ID:SU000601
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Subject Comments:220 subjects
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Current Malaria Infection Prior Malaria Infection Chloroquine Resistance
SA0304449991200046None N/A N/A
SA0304459991200047None N/A N/A
SA0304469991200048None N/A N/A
SA0304479991200045None N/A N/A
SA0304489991200049None N/A N/A
SA0304499991200042None N/A N/A
SA0304509991200043None N/A N/A
SA0304519991100022None N/A N/A
SA0304529991200050None N/A N/A
SA0304539991200055None N/A N/A
SA0304549991200056None N/A N/A
SA0304559991200054None N/A N/A
SA0304569991200053None N/A N/A
SA0304579991200051None N/A N/A
SA0304589991200052None N/A N/A
SA0304599991100021None N/A N/A
SA0304602129347None N/A N/A
SA0304612129340None N/A N/A
SA030462853678None N/A N/A
SA0304632129343None N/A N/A
SA0304642129339None N/A N/A
SA0304652129337None N/A N/A
SA0304662129341None N/A N/A
SA0304672129336None N/A N/A
SA0304682127215None N/A N/A
SA0304692129345None N/A N/A
SA0304702129338None N/A N/A
SA0304712129335None N/A N/A
SA0304722129346None N/A N/A
SA0304732129344None N/A N/A
SA0304742129342None N/A N/A
SA0304759991200057None N/A N/A
SA0304769991200044None N/A N/A
SA0304779991200041None N/A N/A
SA0304789991200062None N/A N/A
SA0304799991200059None N/A N/A
SA0304809991200058None N/A N/A
SA0304819991200061None N/A N/A
SA0304829991200060None N/A N/A
SA0304832016026None NO N/A
SA0304842016019None NO N/A
SA0304852016020None NO N/A
SA0304862016025None NO N/A
SA0304872016024None NO N/A
SA0304882016021None NO N/A
SA0304892016022None NO N/A
SA0304902016015None NO N/A
SA0304912016011None NO N/A
SA0304922016010None NO N/A
SA0304932016008None NO N/A
SA0304942016007None NO N/A
SA0304952016013None NO N/A
SA0304962016012None NO N/A
SA0304972016014None NO N/A
SA0304982016009None YES N/A
SA0304992016016None YES N/A
SA0305002016018None YES N/A
SA0305012016023None YES N/A
SA0305022016017None YES N/A
SA0305032008652P.Vivax N/A Resistant
SA0305042008613P.Vivax N/A Resistant
SA0305052008676P.Vivax N/A Resistant
SA0305062008629P.Vivax N/A Resistant
SA0305072008625P.Vivax N/A Resistant
SA0305082009263P.Vivax N/A Resistant
SA0305092008674P.Vivax N/A Resistant
SA0305102009255P.Vivax N/A Resistant
SA0305112009203P.Vivax N/A Resistant
SA0305122009249P.Vivax N/A Resistant
SA0305132009226P.Vivax N/A Resistant
SA0305142008699P.Vivax N/A Resistant
SA0305152008712P.Vivax N/A Resistant
SA0305162009267P.Vivax N/A Resistant
SA0305172008727P.Vivax N/A Resistant
SA0305182008660P.Vivax N/A Susceptible
SA0305192008654P.Vivax N/A Susceptible
SA0305202008651P.Vivax N/A Susceptible
SA0305212008631P.Vivax N/A Susceptible
SA0305222008627P.Vivax N/A Susceptible
SA0305232008710P.Vivax N/A Susceptible
SA0305242008618P.Vivax N/A Susceptible
SA0305252008603P.Vivax N/A Susceptible
SA0305262008622P.Vivax N/A Susceptible
SA0305272008623P.Vivax N/A Susceptible
SA0305282007278P.Vivax N/A Susceptible
SA0305292008624P.Vivax N/A Susceptible
SA0305302008628P.Vivax N/A Susceptible
SA0305312008621P.Vivax N/A Susceptible
SA0305322009254P.Vivax N/A Susceptible
SA0305332009253P.Vivax N/A Susceptible
SA0305342008722P.Vivax N/A Susceptible
SA0305352008680P.Vivax N/A Susceptible
SA0305362008679P.Vivax N/A Susceptible
SA0305372009261P.Vivax N/A Susceptible
SA0305382009265P.Vivax N/A Susceptible
SA0305392008678P.Vivax N/A Susceptible
SA0305402009262P.Vivax N/A Susceptible
SA0305412009266P.Vivax N/A Susceptible
SA0305422009233P.Vivax N/A Susceptible
SA0305432009109P.Vivax N/A Susceptible
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 273

Collection:

Collection ID:CO000595
Collection Summary:none
Sample Type:Blood
Collection Frequency:Once or Twice

Treatment:

Treatment ID:TR000615
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000608
Sampleprep Summary:aliquots of 30ul sample were mixed with 100ul acetonitrile and 2.5ul internal standard. Keep on ice for 30 minutes and vortex every 15 minutes. Centrifuge for 10 minutes at 13.2rpm and 4C. Using a pipette, 100ul of supernatant was removed and placed into autosampler vials for the mass spectrometer.
Sampleprep Protocol Filename:Metab_Sample_Preparation_Plasma_serum_v1_May_17_2013.docx
Processing Method:Precipitation of protein, centrifuge, and remove supernatant
Processing Storage Conditions:on ice
Extraction Method:1:2 sample:acetonitrile
Extract Storage:Pipette supernatant into autosampler vials for mass spectrometer
Sample Spiking:C18 standards: Caffeine and Diethyl-toluamide. Stable isotopes: [13C6]-D-glucose, [15N]-indole, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [15N]-choline chloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,4-13C2]-cholesterol, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine.

Combined analysis:

Analysis ID AN000888 AN000889
Analysis type MS MS
Chromatography type Reversed phase Ion exchange
Chromatography system Thermo Accela CTC Thermo Accela CTC
Column Thermo Higgins C18 (100 x 2.1mm,2.6um) Hamilton Anion Exchange HPLCs,100x2.1,2.6m,Thermo Fisher
MS Type ESI ESI
MS instrument type Single quadrupole Single quadrupole
MS instrument name Thermo LTQ-FT Thermo LTQ-FT
Ion Mode POSITIVE POSITIVE
Units unspecified unspecified

Chromatography:

Chromatography ID:CH000631
Chromatography Summary:Positive untargeted chromatography (C18 column)
Methods Filename:Metab_Orbitrap_Setup_v2_26Jun2013.docx
Instrument Name:Thermo Accela CTC
Column Name:Thermo Higgins C18 (100 x 2.1mm,2.6um)
Column Temperature:30
Flow Gradient:A: 0-2mins = 90%, 2-7mins = gradient to 0%, 7-10mins = 0%. B: 0-2mins = 5%, 2-7mins = gradient to 95%, 7-10mins = 95%. C: 0-10mins = 5%
Flow Rate:350uL/min
Internal Standard:Caffeine, Diethyl-toluamide
Internal Standard Mt:1.5 min, 6-6.6 min
Sample Injection:10uL
Sampling Cone:HESI probe with S-lens combination for ESI
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:10 minutes
Capillary Voltage:4.6 kV
Oven Temperature:45 C
Running Voltage:45
Weak Wash Solvent Name:H20 with 10% methanol
Sample Syringe Size:20uL
Chromatography Type:Reversed phase
  
Chromatography ID:CH000632
Chromatography Summary:Positive untargeted anion exchange chromatography (AE column)
Methods Filename:Metab_Orbitrap_Setup_v1_May_17_2013.docx
Instrument Name:Thermo Accela CTC
Column Name:Hamilton Anion Exchange HPLCs,100x2.1,2.6m,Thermo Fisher
Column Temperature:30
Flow Gradient:A: 0-2mins = 10%, 2-7mins = gradient to 80%, 7-10mins = 80%. B: 0-2mins = 80%, 2-7mins = gradient to 10%, 7-10mins = 10%. C: 0-10mins = 10%
Flow Rate:350uL/min
Internal Standard:[13C6]-D-glucose, [15N]-indole, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [15N]-choline chloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,4-13C2]-cholesterol, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine
Sample Injection:10uL
Sampling Cone:HESI probe with S-lens combination for ESI
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:10 minutes
Capillary Voltage:4.6 kV
Oven Temperature:45 C
Running Voltage:45
Weak Wash Solvent Name:H20 with 10% methanol
Sample Syringe Size:20uL
Chromatography Type:Ion exchange

MS:

MS ID:MS000790
Analysis ID:AN000888
Instrument Name:Thermo LTQ-FT
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:C18 Pos: technical triplicates for each sample
Ion Mode:POSITIVE
Capillary Voltage:4.45
Collision Gas:N2
Gas Pressure:50
Ionization:electrospray ionization
Mass Accuracy:5 ppm
Source Temperature:48
Spray Voltage:3.5
Atom Gun Current:1000000
Dataformat:.raw, .cdf
Probe Tip:HESI
Resolution Setting:60000
Scan Range Moverz:85-2000
Analysis Protocol File:Metab_Orbitrap_Setup_v2_26Jun2013.docx
  
MS ID:MS000791
Analysis ID:AN000889
Instrument Name:Thermo LTQ-FT
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:Anion exchange Pos: technical triplicates for each sample
Ion Mode:POSITIVE
Capillary Voltage:4.45
Collision Gas:N2
Gas Pressure:50
Ionization:electrospray ionization
Mass Accuracy:5 ppm
Source Temperature:48
Spray Voltage:3.5
Atom Gun Current:1000000
Dataformat:.raw, .cdf
Probe Tip:HESI
Resolution Setting:60000
Scan Range Moverz:85-2000
Analysis Protocol File:Metab_Orbitrap_Setup_v2_26Jun2013.docx
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