Summary of Study ST000515

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.

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Study ID	ST000515
Study Title	Metabolomics of longitudinal plasma samples from Macaca mulatta infected with Plasmodium cynomolgi B 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Study Summary	ATTENTION: The dataset package associated with this study is out of date.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/MTBLS517 for the latest and final version of all files. Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, 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 selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs Primaquine and Chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and during seven-time point collections of venous blood. Supplemental files, including a ReadMe with additional experimental details, all raw data, and analytical metadata, are provided as part of this submission.
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	mahpic@emory.edu
Phone	N/A
Submit Date	2016-11-23
Total Subjects	5
Study Comments	Malaria Host Pathogen Interaction Center Experiment 04, 5 subjects 286 samples. 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). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04). To access other publicly available results from E04 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:	SU000537
Subject Type:	Animal
Subject Species:	Macaca mulatta
Taxonomy ID:	9544
Age Or Age Range:	N/A\| N/A\| ~3years\| ~3years\| ~3years\| ~3years\| ~3years
Weight Or Weight Range:	N/A\| N/A\| 6.05 kg\| 6.05 kg\| 6.05 kg\| 6.05 kg\| 6.05 kg
Gender:	Male\| Male\| Male\| Male\| Male\| Male\| Male
Subject Comments:	Transfusion Donor\| Reference Animal\| Experimental Subject\|Experimental Subject\| Experimental Subject\| Experimental Subject\| Experimental Subject
Species Group:	Mammal

Factors:

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

mb_sample_id	local_sample_id	Gender
SA026765	1979579	Male \| Prior Infection:None \| Days since Inoculation:1
SA026766	1979551	Male \| Prior Infection:None \| Days since Inoculation:1
SA026767	1979561	Male \| Prior Infection:None \| Days since Inoculation:1
SA026768	1979546	Male \| Prior Infection:None \| Days since Inoculation:1
SA026769	1979556	Male \| Prior Infection:None \| Days since Inoculation:1
SA026760	1975092	Male \| Prior Infection:None \| Days since Inoculation:-1
SA026761	1975086	Male \| Prior Infection:None \| Days since Inoculation:-1
SA026762	1975080	Male \| Prior Infection:None \| Days since Inoculation:-1
SA026763	1975125	Male \| Prior Infection:None \| Days since Inoculation:-1
SA026764	1975020	Male \| Prior Infection:None \| Days since Inoculation:-1
SA026770	2058598	Male \| Prior Infection:None \| Days since Inoculation:104
SA026771	2058603	Male \| Prior Infection:None \| Days since Inoculation:104
SA026772	2058593	Male \| Prior Infection:None \| Days since Inoculation:104
SA026773	2058588	Male \| Prior Infection:None \| Days since Inoculation:104
SA026774	2060792	Male \| Prior Infection:None \| Days since Inoculation:106
SA026775	2060782	Male \| Prior Infection:None \| Days since Inoculation:106
SA026776	2060797	Male \| Prior Infection:None \| Days since Inoculation:106
SA026777	2060787	Male \| Prior Infection:None \| Days since Inoculation:106
SA026778	1986957	Male \| Prior Infection:None \| Days since Inoculation:11
SA026779	1986947	Male \| Prior Infection:None \| Days since Inoculation:11
SA026780	1986942	Male \| Prior Infection:None \| Days since Inoculation:11
SA026781	1986962	Male \| Prior Infection:None \| Days since Inoculation:11
SA026782	1986952	Male \| Prior Infection:None \| Days since Inoculation:11
SA026783	1988270	Male \| Prior Infection:None \| Days since Inoculation:13
SA026784	1988255	Male \| Prior Infection:None \| Days since Inoculation:13
SA026785	1988260	Male \| Prior Infection:None \| Days since Inoculation:13
SA026786	1988250	Male \| Prior Infection:None \| Days since Inoculation:13
SA026787	1988265	Male \| Prior Infection:None \| Days since Inoculation:13
SA026788	1990896	Male \| Prior Infection:None \| Days since Inoculation:15
SA026789	1990901	Male \| Prior Infection:None \| Days since Inoculation:15
SA026790	1990911	Male \| Prior Infection:None \| Days since Inoculation:15
SA026791	1990916	Male \| Prior Infection:None \| Days since Inoculation:15
SA026792	1990906	Male \| Prior Infection:None \| Days since Inoculation:15
SA026793	1991821	Male \| Prior Infection:None \| Days since Inoculation:17
SA026794	1991841	Male \| Prior Infection:None \| Days since Inoculation:17
SA026795	1991836	Male \| Prior Infection:None \| Days since Inoculation:17
SA026796	1991831	Male \| Prior Infection:None \| Days since Inoculation:17
SA026797	1991826	Male \| Prior Infection:None \| Days since Inoculation:17
SA026798	1991880	Male \| Prior Infection:None \| Days since Inoculation:18
SA026799	1993046	Male \| Prior Infection:None \| Days since Inoculation:19
SA026800	1993026	Male \| Prior Infection:None \| Days since Inoculation:19
SA026801	1993036	Male \| Prior Infection:None \| Days since Inoculation:19
SA026802	1993031	Male \| Prior Infection:None \| Days since Inoculation:19
SA026803	1993041	Male \| Prior Infection:None \| Days since Inoculation:19
SA026804	1995832	Male \| Prior Infection:None \| Days since Inoculation:20
SA026805	1995844	Male \| Prior Infection:None \| Days since Inoculation:20
SA026806	1995910	Male \| Prior Infection:None \| Days since Inoculation:21
SA026807	1996024	Male \| Prior Infection:None \| Days since Inoculation:21
SA026808	1996019	Male \| Prior Infection:None \| Days since Inoculation:21
SA026809	1996029	Male \| Prior Infection:None \| Days since Inoculation:21
SA026810	1995922	Male \| Prior Infection:None \| Days since Inoculation:21
SA026811	1998663	Male \| Prior Infection:None \| Days since Inoculation:23
SA026812	1998668	Male \| Prior Infection:None \| Days since Inoculation:23
SA026813	1998957	Male \| Prior Infection:None \| Days since Inoculation:23
SA026814	1998658	Male \| Prior Infection:None \| Days since Inoculation:23
SA026815	1998648	Male \| Prior Infection:None \| Days since Inoculation:23
SA026816	1999114	Male \| Prior Infection:None \| Days since Inoculation:25
SA026817	1999129	Male \| Prior Infection:None \| Days since Inoculation:25
SA026818	1999119	Male \| Prior Infection:None \| Days since Inoculation:25
SA026819	1999124	Male \| Prior Infection:None \| Days since Inoculation:25
SA026820	1999443	Male \| Prior Infection:None \| Days since Inoculation:26
SA026821	1999442	Male \| Prior Infection:None \| Days since Inoculation:26
SA026822	1999441	Male \| Prior Infection:None \| Days since Inoculation:26
SA026823	1999440	Male \| Prior Infection:None \| Days since Inoculation:26
SA026824	2003641	Male \| Prior Infection:None \| Days since Inoculation:27
SA026825	2003636	Male \| Prior Infection:None \| Days since Inoculation:27
SA026826	2003626	Male \| Prior Infection:None \| Days since Inoculation:27
SA026827	2003631	Male \| Prior Infection:None \| Days since Inoculation:27
SA026828	2005641	Male \| Prior Infection:None \| Days since Inoculation:29
SA026829	2005631	Male \| Prior Infection:None \| Days since Inoculation:29
SA026830	2005646	Male \| Prior Infection:None \| Days since Inoculation:29
SA026831	2005636	Male \| Prior Infection:None \| Days since Inoculation:29
SA026832	1981033	Male \| Prior Infection:None \| Days since Inoculation:3
SA026833	1981038	Male \| Prior Infection:None \| Days since Inoculation:3
SA026834	1981028	Male \| Prior Infection:None \| Days since Inoculation:3
SA026835	1981043	Male \| Prior Infection:None \| Days since Inoculation:3
SA026836	1981023	Male \| Prior Infection:None \| Days since Inoculation:3
SA026837	2005900	Male \| Prior Infection:None \| Days since Inoculation:31
SA026838	2005895	Male \| Prior Infection:None \| Days since Inoculation:31
SA026839	2005905	Male \| Prior Infection:None \| Days since Inoculation:31
SA026840	2005890	Male \| Prior Infection:None \| Days since Inoculation:31
SA026841	2006389	Male \| Prior Infection:None \| Days since Inoculation:33
SA026842	2006384	Male \| Prior Infection:None \| Days since Inoculation:33
SA026843	2006379	Male \| Prior Infection:None \| Days since Inoculation:33
SA026844	2006374	Male \| Prior Infection:None \| Days since Inoculation:33
SA026845	2008343	Male \| Prior Infection:None \| Days since Inoculation:35
SA026846	2008338	Male \| Prior Infection:None \| Days since Inoculation:35
SA026847	2008333	Male \| Prior Infection:None \| Days since Inoculation:35
SA026848	2008328	Male \| Prior Infection:None \| Days since Inoculation:35
SA026849	2010130	Male \| Prior Infection:None \| Days since Inoculation:37
SA026850	2010125	Male \| Prior Infection:None \| Days since Inoculation:37
SA026851	2010135	Male \| Prior Infection:None \| Days since Inoculation:37
SA026852	2010120	Male \| Prior Infection:None \| Days since Inoculation:37
SA026853	2010684	Male \| Prior Infection:None \| Days since Inoculation:39
SA026854	2010679	Male \| Prior Infection:None \| Days since Inoculation:39
SA026855	2010674	Male \| Prior Infection:None \| Days since Inoculation:39
SA026856	2010689	Male \| Prior Infection:None \| Days since Inoculation:39
SA026857	2012632	Male \| Prior Infection:None \| Days since Inoculation:41
SA026858	2012642	Male \| Prior Infection:None \| Days since Inoculation:41
SA026859	2012627	Male \| Prior Infection:None \| Days since Inoculation:41

Showing page 1 of 3 Results: 1 2 3 Next Showing results 1 to 100 of 286

Collection:

Collection ID:	CO000531
Collection Summary:	Every Other Day Collection\|Time Point 1 - Baseline: Uninfected control for each 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 may be severe or non-severe. NHPs were monitored, and clinical interventions were performed as necessary. Otherwise, NHPs self-resolved infection.\|Time Point 3 - Post-Peak of Infection: Observations 7 days after peak infection.\|Time Point 4 - 1st Relapse Peak of Infection: This time point tested expectations of a mild drop in hemoglobin levels and low parasitemias relative to peak infection arising from activation of hypnozoites. \|Time Point 5 - Post-Peak of 1st Relapse Infection: Inter-relapse interval. \|Time Point 6 - 2nd Relapse Peak of Infection: Same goal as time point 4 for 2nd relapse.\|Time Point 7 - Post-Peak of 2nd Relapse Infection: Observations on NHP response after a second relapse infection.
Sample Type:	Whole blood
Collection Method:	Ear Prick\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous\|Intravenous
Collection Time:	Every Other Day\|Once\|Once\|Once\|Once\|Once\|Once\|Once
Blood Serum Or Plasma:	Plasma

Treatment:

Treatment ID:	TR000551
Treatment Summary:	Plasmodium Cynomolgi Strain B Sporozoites Inoculation
Treatment:	Biotic
Treatment Route:	Injection

Sample Preparation:

Sampleprep ID:	SP000544
Sampleprep Summary:	aliquots of 65ul sample were mixed with 130ul acetonitrile and 3.25ul internal standard. Keep on ice and vortex every 15 minutes. Centrifuge for 10 minutes at 13.2rpm and 4C. Using a pipette, 130ul 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 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 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	AN000788	AN000789
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo QExactive	Thermo QExactive
Column	Higgins C18 (100 x 2.1mm,5um)	Higgins C18 (100 x 2.1mm,5um)
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	peak intensity	peak intensity

Chromatography:

Chromatography ID:	CH000565
Chromatography Summary:	untargeted chromatography (C18 column)
Methods Filename:	Metab_Orbitrap_Setup_v1_May_17_2013.docx
Chromatography Comments:	Thermo QExactive coupled to CTC PAL HTC Accela1-TMO autosampler
Instrument Name:	Thermo QExactive
Column Name:	Higgins C18 (100 x 2.1mm,5um)
Column Pressure:	200 Bar (max)
Column Temperature:	30
Flow Gradient:	A%: 0-10mins = 5%; B%: 0-2mins = 35%, 2-7mins = gradient to 95%, 7-10mins = 95%; C%: 0-2mins = 60%, 2-7mins = gradient to 0%, 7-10mins = 0%
Flow Rate:	0-2mins = 350 μL/min, 2-7mins = gradient to 400 μL/min, 7-10mins = 400 μL/min
Injection Temperature:	4C
Internal Standard:	Caffeine, Diethyl-toluamide
Internal Standard Mt:	1.5 min; 6-6.6 min
Sample Injection:	10μL
Sampling Cone:	ESI: HESI probe with S-lens combination
Solvent A:	100% water; 0.2% formic acid
Solvent B:	100% acetonitrile
Analytical Time:	10 minutes
Capillary Voltage:	4.6 kV
Oven Temperature:	45C
Running Voltage:	4.6 kV
Weak Wash Solvent Name:	H20 with 10% methanol
Weak Wash Volume:	20μL
Chromatography Type:	Reversed phase

MS:

MS ID:	MS000695
Analysis ID:	AN000788
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
Ion Mode:	POSITIVE
Capillary Temperature:	250
Capillary Voltage:	4.45
Collision Gas:	N2
Gas Pressure:	50 PSI
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:	120,000
Scan Range Moverz:	85-1275
Analysis Protocol File:	Metabolomics_Core_Data_Analysis.docx

MS ID:	MS000696
Analysis ID:	AN000789
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
Ion Mode:	NEGATIVE
Capillary Temperature:	250
Capillary Voltage:	4.45
Collision Gas:	N2
Gas Pressure:	50 PSI
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:	120,000
Scan Range Moverz:	85-1275
Analysis Protocol File:	Metabolomics_Core_Data_Analysis.docx