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.
Study ID | ST000578 |
Study Title | Experiment HuA: Metabolomics of plasma samples from humans infected with Plasmodium vivax strain. |
Study Type | Longitudinal study and treatment of multiple individuals with Chloroquine |
Study Summary | Patients 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 |
Department | School of Medicine, Vaccine Center at Yerkes |
Last Name | Galinksi |
First Name | Mary |
Address | Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329 |
mahpic@emory.edu | |
Phone | None |
Submit Date | 2017-02-20 |
Num Groups | 273 |
Total Subjects | 220 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2017-07-10 |
Release Version | 1 |
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: | Mammals |
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 |
---|---|---|---|---|
SA030444 | 9991200046 | None | N/A | N/A |
SA030445 | 9991200047 | None | N/A | N/A |
SA030446 | 9991200048 | None | N/A | N/A |
SA030447 | 9991200045 | None | N/A | N/A |
SA030448 | 9991200049 | None | N/A | N/A |
SA030449 | 9991200042 | None | N/A | N/A |
SA030450 | 9991200043 | None | N/A | N/A |
SA030451 | 9991100022 | None | N/A | N/A |
SA030452 | 9991200050 | None | N/A | N/A |
SA030453 | 9991200055 | None | N/A | N/A |
SA030454 | 9991200056 | None | N/A | N/A |
SA030455 | 9991200054 | None | N/A | N/A |
SA030456 | 9991200053 | None | N/A | N/A |
SA030457 | 9991200051 | None | N/A | N/A |
SA030458 | 9991200052 | None | N/A | N/A |
SA030459 | 9991100021 | None | N/A | N/A |
SA030460 | 2129347 | None | N/A | N/A |
SA030461 | 2129340 | None | N/A | N/A |
SA030462 | 853678 | None | N/A | N/A |
SA030463 | 2129343 | None | N/A | N/A |
SA030464 | 2129339 | None | N/A | N/A |
SA030465 | 2129337 | None | N/A | N/A |
SA030466 | 2129341 | None | N/A | N/A |
SA030467 | 2129336 | None | N/A | N/A |
SA030468 | 2127215 | None | N/A | N/A |
SA030469 | 2129345 | None | N/A | N/A |
SA030470 | 2129338 | None | N/A | N/A |
SA030471 | 2129335 | None | N/A | N/A |
SA030472 | 2129346 | None | N/A | N/A |
SA030473 | 2129344 | None | N/A | N/A |
SA030474 | 2129342 | None | N/A | N/A |
SA030475 | 9991200057 | None | N/A | N/A |
SA030476 | 9991200044 | None | N/A | N/A |
SA030477 | 9991200041 | None | N/A | N/A |
SA030478 | 9991200062 | None | N/A | N/A |
SA030479 | 9991200059 | None | N/A | N/A |
SA030480 | 9991200058 | None | N/A | N/A |
SA030481 | 9991200061 | None | N/A | N/A |
SA030482 | 9991200060 | None | N/A | N/A |
SA030483 | 2016026 | None | NO | N/A |
SA030484 | 2016019 | None | NO | N/A |
SA030485 | 2016020 | None | NO | N/A |
SA030486 | 2016025 | None | NO | N/A |
SA030487 | 2016024 | None | NO | N/A |
SA030488 | 2016021 | None | NO | N/A |
SA030489 | 2016022 | None | NO | N/A |
SA030490 | 2016015 | None | NO | N/A |
SA030491 | 2016011 | None | NO | N/A |
SA030492 | 2016010 | None | NO | N/A |
SA030493 | 2016008 | None | NO | N/A |
SA030494 | 2016007 | None | NO | N/A |
SA030495 | 2016013 | None | NO | N/A |
SA030496 | 2016012 | None | NO | N/A |
SA030497 | 2016014 | None | NO | N/A |
SA030498 | 2016009 | None | YES | N/A |
SA030499 | 2016016 | None | YES | N/A |
SA030500 | 2016018 | None | YES | N/A |
SA030501 | 2016023 | None | YES | N/A |
SA030502 | 2016017 | None | YES | N/A |
SA030503 | 2008652 | P.Vivax | N/A | Resistant |
SA030504 | 2008613 | P.Vivax | N/A | Resistant |
SA030505 | 2008676 | P.Vivax | N/A | Resistant |
SA030506 | 2008629 | P.Vivax | N/A | Resistant |
SA030507 | 2008625 | P.Vivax | N/A | Resistant |
SA030508 | 2009263 | P.Vivax | N/A | Resistant |
SA030509 | 2008674 | P.Vivax | N/A | Resistant |
SA030510 | 2009255 | P.Vivax | N/A | Resistant |
SA030511 | 2009203 | P.Vivax | N/A | Resistant |
SA030512 | 2009249 | P.Vivax | N/A | Resistant |
SA030513 | 2009226 | P.Vivax | N/A | Resistant |
SA030514 | 2008699 | P.Vivax | N/A | Resistant |
SA030515 | 2008712 | P.Vivax | N/A | Resistant |
SA030516 | 2009267 | P.Vivax | N/A | Resistant |
SA030517 | 2008727 | P.Vivax | N/A | Resistant |
SA030518 | 2008660 | P.Vivax | N/A | Susceptible |
SA030519 | 2008654 | P.Vivax | N/A | Susceptible |
SA030520 | 2008651 | P.Vivax | N/A | Susceptible |
SA030521 | 2008631 | P.Vivax | N/A | Susceptible |
SA030522 | 2008627 | P.Vivax | N/A | Susceptible |
SA030523 | 2008710 | P.Vivax | N/A | Susceptible |
SA030524 | 2008618 | P.Vivax | N/A | Susceptible |
SA030525 | 2008603 | P.Vivax | N/A | Susceptible |
SA030526 | 2008622 | P.Vivax | N/A | Susceptible |
SA030527 | 2008623 | P.Vivax | N/A | Susceptible |
SA030528 | 2007278 | P.Vivax | N/A | Susceptible |
SA030529 | 2008624 | P.Vivax | N/A | Susceptible |
SA030530 | 2008628 | P.Vivax | N/A | Susceptible |
SA030531 | 2008621 | P.Vivax | N/A | Susceptible |
SA030532 | 2009254 | P.Vivax | N/A | Susceptible |
SA030533 | 2009253 | P.Vivax | N/A | Susceptible |
SA030534 | 2008722 | P.Vivax | N/A | Susceptible |
SA030535 | 2008680 | P.Vivax | N/A | Susceptible |
SA030536 | 2008679 | P.Vivax | N/A | Susceptible |
SA030537 | 2009261 | P.Vivax | N/A | Susceptible |
SA030538 | 2009265 | P.Vivax | N/A | Susceptible |
SA030539 | 2008678 | P.Vivax | N/A | Susceptible |
SA030540 | 2009262 | P.Vivax | N/A | Susceptible |
SA030541 | 2009266 | P.Vivax | N/A | Susceptible |
SA030542 | 2009233 | P.Vivax | N/A | Susceptible |
SA030543 | 2009109 | P.Vivax | N/A | Susceptible |
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 |