Summary of Study ST000599

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 ID	ST000599
Study Title	Metabolomics measures of Macaca mulatta infected with Plasmodium coatneyi Hackeri strain
Study Type	Longitudinal parasite infection and treatment of multiple individuals
Study Summary	ATTENTION: The dataset package associated with this study is out of date. Please refer to https://www.ebi.ac.uk/metabolights/MTBLS518 for the latest and final version of all files. Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks. The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 100 days. The different clinical phases of the infection were clinically determined for each subject. Blood-stage curative doses of artemether were administered to all subjects at the end of the study. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 03’. This dataset was produced by Dean Jones at Emory University. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
Institute	Emory University
Department	School of Medicine, Vaccine Center at Yerkes
Last Name	Galinski
First Name	Mary
Address	Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
Email	mahpic@emory.edu
Phone	N/A
Submit Date	2017-03-23
Num Groups	6
Total Subjects	331
Study Comments	The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). Contributors include: Monica Cabrera, Jeremy D. DeBarry, Mary G. Galinski, Jay Humphrey, Dean Jones, Ebru Karpuzoglu, Jessica C. Kissinger, Regina Joice, Esmeralda Meyer, Vishal Nayak, Mustafa Nural, Suman Pakala, ViLinh Tran, Karan Uppal, Loukia Williams. For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 03' (E03). To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public.
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:	SU000622
Subject Type:	Animal
Subject Species:	Macaca mulatta
Taxonomy ID:	9544
Weight Or Weight Range:	NA\|6.94kg\|9.04kg\|8.03kg\|8.83kg\|8.68kg
Gender:	Male\|Male\|Male\|Male\|Male\|Male
Animal Animal Supplier:	Yerkes Field Station\|Yerkes Field Station\|Yerkes Primate Research Center\|Yerkes Primate Research Center\|\|Yerkes Primate Research Center
Animal Housing:	Metallic\|Metallic\|Metallic\|Metallic\|Metallic\|Metallic
Animal Light Cycle:	12/12\|12/12\|12/12\|12/12\|12/12\|12/12
Animal Feed:	Monkey Jumbo Diet 5037 and 5038\|Monkey Jumbo Diet 5037 and 5038\|Monkey Jumbo Diet 5037 and 5038\|Monkey Jumbo Diet 5037 and 5038\|Monkey Jumbo Diet 5037 and 5038\|Monkey Jumbo Diet 5037 and 5038
Animal Water:	tap in bottle\|tap in bottle\|tap in bottle\|tap in bottle\|tap in bottle\|tap in bottle
Animal Inclusion Criteria:	Weight\|Weight\|Weight\|Weight\|Weight\|Weight
Species Group:	Mammals

Factors:

Subject type: Animal; Subject species: Macaca mulatta (Factor headings shown in green)

mb_sample_id	local_sample_id	Gender	Prior Infection	Days since Inoculation	Collection Type
SA032782	2182540	Male	N/A	N/A	Reference
SA032788	2206590	Male	None	100	Every Other Day
SA032789	2206585	Male	None	100	Every Other Day
SA032790	2206595	Male	None	100	Every Other Day
SA032791	2206605	Male	None	100	Every Other Day
SA032792	2206600	Male	None	100	Every Other Day
SA032793	2129582	Male	None	10	Every Other Day
SA032794	2129592	Male	None	10	Every Other Day
SA032795	2129597	Male	None	10	Every Other Day
SA032796	2129577	Male	None	10	Every Other Day
SA032797	2129996	Male	None	12	Every Other Day
SA032798	2130006	Male	None	12	Every Other Day
SA032799	2129991	Male	None	12	Every Other Day
SA032800	2130001	Male	None	12	Every Other Day
SA032801	2129986	Male	None	12	Every Other Day
SA032802	2131265	Male	None	14	Every Other Day
SA032803	2131245	Male	None	14	Every Other Day
SA032804	2131250	Male	None	14	Every Other Day
SA032805	2131260	Male	None	14	Every Other Day
SA032806	2131255	Male	None	14	Every Other Day
SA032807	2133243	Male	None	16	Every Other Day
SA032808	2133253	Male	None	16	Every Other Day
SA032809	2133248	Male	None	16	Every Other Day
SA032810	2133258	Male	None	16	Every Other Day
SA032811	2133263	Male	None	16	Every Other Day
SA032812	2134982	Male	None	18	Every Other Day
SA032813	2134972	Male	None	18	Every Other Day
SA032814	2134962	Male	None	18	Every Other Day
SA032815	2134967	Male	None	18	Every Other Day
SA032816	2134977	Male	None	18	Every Other Day
SA032817	2135348	Male	None	20	Every Other Day
SA032818	2135353	Male	None	20	Every Other Day
SA032819	2135343	Male	None	20	Every Other Day
SA032820	2135363	Male	None	20	Every Other Day
SA032821	2135358	Male	None	20	Every Other Day
SA032822	2137695	Male	None	22	Every Other Day
SA032823	2137690	Male	None	22	Every Other Day
SA032824	2137920	Male	None	22	Time Point 2
SA032825	2137919	Male	None	22	Time Point 2
SA032826	2139058	Male	None	22	Time Point 2
SA032827	2137921	Male	None	22	Time Point 2
SA032828	2139946	Male	None	24	Every Other Day
SA032829	2139951	Male	None	24	Every Other Day
SA032830	2139956	Male	None	24	Every Other Day
SA032831	2139966	Male	None	24	Every Other Day
SA032832	2139961	Male	None	24	Every Other Day
SA032833	2140057	Male	None	26	Every Other Day
SA032834	2140072	Male	None	26	Every Other Day
SA032835	2140067	Male	None	26	Every Other Day
SA032836	2140062	Male	None	26	Every Other Day
SA032837	2140077	Male	None	26	Every Other Day
SA032838	2140904	Male	None	28	Every Other Day
SA032839	2140914	Male	None	28	Every Other Day
SA032840	2140924	Male	None	28	Every Other Day
SA032841	2140909	Male	None	28	Every Other Day
SA032842	2140919	Male	None	28	Every Other Day
SA032843	2140769	Male	None	29	Time Point 2
SA032844	2142020	Male	None	29	Time Point 3
SA032845	2142008	Male	None	29	Time Point 3
SA032846	2124863	Male	None	2	Every Other Day
SA032847	2124853	Male	None	2	Every Other Day
SA032848	2124858	Male	None	2	Every Other Day
SA032849	2124843	Male	None	2	Every Other Day
SA032850	2124848	Male	None	2	Every Other Day
SA032851	2143361	Male	None	30	Every Other Day
SA032852	2143346	Male	None	30	Every Other Day
SA032853	2143351	Male	None	30	Every Other Day
SA032854	2143356	Male	None	30	Every Other Day
SA032855	2143366	Male	None	30	Every Other Day
SA032856	2142181	Male	None	31	Time Point 3
SA032857	2142160	Male	None	31	Time Point 3
SA032858	2144087	Male	None	32	Every Other Day
SA032859	2144082	Male	None	32	Every Other Day
SA032860	2144092	Male	None	32	Every Other Day
SA032861	2144077	Male	None	32	Every Other Day
SA032862	2144072	Male	None	32	Every Other Day
SA032863	2145347	Male	None	34	Every Other Day
SA032864	2145342	Male	None	34	Every Other Day
SA032865	2145337	Male	None	34	Every Other Day
SA032866	2145332	Male	None	34	Every Other Day
SA032867	2145352	Male	None	34	Every Other Day
SA032868	2147319	Male	None	36	Every Other Day
SA032869	2147309	Male	None	36	Every Other Day
SA032870	2147304	Male	None	36	Every Other Day
SA032871	2147299	Male	None	36	Every Other Day
SA032872	2147314	Male	None	36	Every Other Day
SA032873	2146735	Male	None	37	Time Point 3
SA032874	2148901	Male	None	38	Every Other Day
SA032875	2148916	Male	None	38	Every Other Day
SA032876	2148896	Male	None	38	Every Other Day
SA032877	2148906	Male	None	38	Every Other Day
SA032878	2148911	Male	None	38	Every Other Day
SA032879	2148974	Male	None	39	Time Point 4
SA032880	2150497	Male	None	40	Every Other Day
SA032881	2150487	Male	None	40	Every Other Day
SA032882	2150492	Male	None	40	Every Other Day
SA032883	2150502	Male	None	40	Every Other Day
SA032884	2150482	Male	None	40	Every Other Day
SA032885	2150985	Male	None	42	Every Other Day
SA032886	2150970	Male	None	42	Every Other Day

Showing page 1 of 4 Results: 1 2 3 4 Next Showing results 1 to 100 of 331

Collection:

Collection ID:	CO000616
Collection Summary:	Every Other Day Collection \| Time Point 1 Baseline: Uninfected control for each Non-Human Primate (NHP). \| Time Point 2 Peak of infection: Peak of infection determined by clinical and parasitological assessment for each NHP. The time point is intended to characterize the host immune response and capture multi-omics data during the peak of parasitemias when the NHP is experiencing clinical signs of disease that are commonly severe in P. coatneyi infections. NHPs were monitored based on clinical and hematological parameters, and clinical interventions with artemether were performed as necessary. \| Time Point 3 Post-peak: Observations 7 days after peak infection and sub-curative treatment. \| Time Point 4 Recrudescence Peak: This time point tested expectations of a drop in hemoglobin levels and increase in parasitemias due to recrudescence from a chronic infection. After sample collection, NHPs received sub-curative treatment with artemether based on clinical and hematological parameters. \| Time Point 5 Post-peak: Chronic infection with low levels of persistent parasitemia that may be below detectable levels. \| Time Point 6 Recrudescence Peak: Same goal as time point 4 for 2nd second recrudescence peak. \| Time Point 7 Post-peak: Observations of NHP response after a second recrudescence in a chronic phase with low levels of persistent parasitemia.
Sample Type:	Whole blood\|Whole blood\|Whole blood\|Whole blood\|Whole blood\|Whole blood\|Whole blood\|Whole blood
Collection Method:	Ear Prick\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous
Collection Frequency:	Every Other Day\|Once\|Once\|Once\|Once\|Once\|Once\|Once
Blood Serum Or Plasma:	Plasma\|Plasma\|Plasma\|Plasma\|Plasma\|Plasma\|Plasma\|Plasma

Treatment:

Treatment ID:	TR000636
Treatment Summary:	Plasmodium Coatneyi Hackeri Strain Sporozoites Inoculation
Treatment:	Biotic
Treatment Route:	Injection

Sample Preparation:

Sampleprep ID:	SP000629
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:	E03_MB_Sample_Preparations_Plasma_serum_HFQE_V1_3282016.docx, E4_E3_E18_E23_E24_E25_MalariaCore_Metabolomics SOP_v1_6October2016.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, Diethyl-toluamide. Internal Standards/Stable Isotopes: [13C6]-D-glucose, [15N]-indole, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine

Combined analysis:

Analysis ID	AN000917	AN000918
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Thermo Accucore C18 (100 x 2.1mm,2.6um)	Thermo Accucore C18 (100 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Ion Intensity	Ion Intensity

Chromatography:

Chromatography ID:	CH000654
Chromatography Summary:	C18 120k resolution method with C18 positive and negative wash
Methods Filename:	Metab_HFQE_Setup.docx
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Thermo Accucore C18 (100 x 2.1mm,2.6um)
Column Pressure:	200 Bar (max)
Column Temperature:	30
Flow Gradient:	A: 0-2mins = 80%, 2-7mins = gradient to 0%, 7-10mins = 0%. B: 0-2mins = 15%, 2-7mins = gradient to 95%, 7-10mins = 95%. C: 0-10mins = 5%
Flow Rate:	350μL/min
Internal Standard:	Cystine; cysteine-glutathione disulfide; carboxymethyl-cysteine (very low); glutathione disulfide (+1 and +2); carboxymethyl-glutathione
Internal Standard Mt:	1.5 min, 6-6.6 min
Sample Injection:	10μL
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:	45C
Weak Wash Solvent Name:	H20 with 10% methanol
Sample Syringe Size:	20μL
Chromatography Type:	Reversed phase

MS:

MS ID:	MS000816
Analysis ID:	AN000917
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Technical triplicates for each sample
Ion Mode:	POSITIVE
Capillary Temperature:	300
Capillary Voltage:	4.45
Collision Gas:	N2
Gas Pressure:	50 psi
Ionization:	electrospray ionization
Mass Accuracy:	5ppm
Source Temperature:	48
Spray Voltage:	3.5
Atom Gun Current:	1000000
Dataformat:	.raw, .cdf
Probe Tip:	HESI
Resolution Setting:	120000
Scan Range Moverz:	85-1275

MS ID:	MS000817
Analysis ID:	AN000918
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
Ion Mode:	NEGATIVE
Capillary Temperature:	300
Capillary Voltage:	4.45
Collision Gas:	N2
Gas Pressure:	50 psi
Ionization:	electrospray ionization
Mass Accuracy:	5ppm
Source Temperature:	48
Spray Voltage:	3.5
Atom Gun Current:	1000000
Dataformat:	.raw, .cdf
Probe Tip:	HESI
Resolution Setting:	120000
Scan Range Moverz:	85-1275