Summary of Study ST004101

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 PR002576. The data can be accessed directly via it's Project DOI: 10.21228/M8P563 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST004101
Study Title	Combined bacterial infection and radiation injury in the murine model: Consequences on metabolomics based biodosimetry (Urine analysis)
Study Summary	High-throughput biodosimetry assays are needed to assess ionizing radiation (IR) exposure in emergency situations that can predict the level of acute radiation syndrome (ARS) across a heterogenous segment of the population that may have secondary bacterial infections or combined injury. In this study, we investigate the impact of bacterial infection on metabolite-based biodosimetry using a well-established model: recombinant Listeria monocytogenes expressing ovalbumin (Lm-OVA) and C57BL/6 murine infection model. Male mice were infected with Lm-OVA, then subjected to 0, 2, or 6 Gy X-ray irradiation at 4 days post-infection (dpi). Biofluids were analyzed using untargeted metabolomics at 1 day (d) post-irradiation (5 dpi).
Institute	Georgetown University
Last Name	Pannkuk
First Name	Evan
Address	3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Email	elp44@georgetown.edu
Phone	2026875650
Submit Date	2025-05-21
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Waters)
Analysis Type Detail	LC-MS
Release Date	2026-01-02
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002576
Project DOI:	doi: 10.21228/M8P563
Project Title:	Combined bacterial infection and radiation injury in the murine model: Consequences on metabolomics based biodosimetry
Project Summary:	High-throughput biodosimetry assays are needed to assess ionizing radiation (IR) exposure in emergency situations that can predict the level of acute radiation syndrome (ARS) across a heterogenous segment of the population that may have secondary bacterial infections or combined injury. In this study, we investigate the impact of bacterial infection on metabolite-based biodosimetry using a well-established model: recombinant Listeria monocytogenes expressing ovalbumin (Lm-OVA) and C57BL/6 murine infection model. Male mice were infected with Lm-OVA, then subjected to 0, 2, or 6 Gy X-ray irradiation at 4 days post-infection (dpi). Biofluids were analyzed using untargeted metabolomics at 1 day (d) post-irradiation (5 dpi).
Institute:	Georgetown University
Last Name:	Pannkuk
First Name:	Evan
Address:	3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Email:	elp44@georgetown.edu
Phone:	2026875650

Subject:

Subject ID:	SU004248
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Male

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Exposure	Irradiation
SA474631	674	Urine	1_NF_Sham	0Gy
SA474632	670	Urine	1_NF_Sham	0Gy
SA474633	669	Urine	1_NF_Sham	0Gy
SA474634	672	Urine	1_NF_Sham	0Gy
SA474635	673	Urine	1_NF_Sham	0Gy
SA474636	671	Urine	1_NF_Sham	0Gy
SA474637	675	Urine	2_NF_2Gy	2Gy
SA474638	676	Urine	2_NF_2Gy	2Gy
SA474639	677	Urine	2_NF_2Gy	2Gy
SA474640	678	Urine	2_NF_2Gy	2Gy
SA474641	679	Urine	2_NF_2Gy	2Gy
SA474642	680	Urine	2_NF_2Gy	2Gy
SA474643	685	Urine	3_NF_6Gy	6Gy
SA474644	686	Urine	3_NF_6Gy	6Gy
SA474645	684	Urine	3_NF_6Gy	6Gy
SA474646	683	Urine	3_NF_6Gy	6Gy
SA474647	682	Urine	3_NF_6Gy	6Gy
SA474648	681	Urine	3_NF_6Gy	6Gy
SA474649	720	Urine	4_Inf_Sham	0Gy
SA474650	719	Urine	4_Inf_Sham	0Gy
SA474651	718	Urine	4_Inf_Sham	0Gy
SA474652	716	Urine	4_Inf_Sham	0Gy
SA474653	715	Urine	4_Inf_Sham	0Gy
SA474654	713	Urine	5_Inf_2Gy	2Gy
SA474655	714	Urine	5_Inf_2Gy	2Gy
SA474656	709	Urine	5_Inf_2Gy	2Gy
SA474657	710	Urine	5_Inf_2Gy	2Gy
SA474658	711	Urine	5_Inf_2Gy	2Gy
SA474659	712	Urine	5_Inf_2Gy	2Gy
SA474660	704	Urine	6_Inf_6Gy	6Gy
SA474661	708	Urine	6_Inf_6Gy	6Gy
SA474662	707	Urine	6_Inf_6Gy	6Gy
SA474663	706	Urine	6_Inf_6Gy	6Gy
SA474664	705	Urine	6_Inf_6Gy	6Gy
SA474665	703	Urine	6_Inf_6Gy	6Gy
SA474666	701	Urine	6_Inf_6Gy	6Gy
SA474667	702	Urine	6_Inf_6Gy	6Gy

Showing results 1 to 37 of 37

Showing results 1 to 37 of 37

Collection:

Collection ID:	CO004241
Collection Summary:	At 1 d post-irradiation, spot urines were collected, blood was collected via cardiac puncture, and serum for metabolomics was separated using BD Microtainer Tubes (REF 365967) with ~100 μL of whole blood added to each tube, kept at room temperature for 30 min, then centrifuged (1300 x g, 4°C) for 10 min. Biofluids were flash frozen and stored at -80°C until analysis. A separate aliquot of blood was collected in a dipotassium EDTA Tube (BD Cat #365974) for collecting complete blood count (CBC including levels of white blood cells [WBC], lymphocyte [LYM], monocyte [MON], and neutrophil [NEU]) by VRL Diagnostics (Gaithersburg, MD, http://www.vrlsat.com/).
Sample Type:	Urine
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004257
Treatment Summary:	All animal experiments were approved by the Georgetown University Institutional Animal Care and Use Committee (IACUC, protocol #2023-0012) and were conducted under all relevant federal and state guidelines. Male C57BL/6 mice (10 weeks old) were purchased from Charles River Laboratories (Frederick, MD) and provided food (PicoLab Rodent Diet 20 #5053) and deionized water was provided ad libitum. Mice were infected with a retro-orbital injection of Lm-OVA, which is a widely used and reproducible infection method as the bacteria can bypass the gut stage of infection. Lm-OVA stocks frozen at -80°C were grown overnight at 37°C while shaking in BHI broth supplemented with 5 µg/mL erythromycin. Then, overnight cultures were sub-cultured by diluting into fresh BHI broth supplemented with 5 µg/mL erythromycin and grown for 4 hours at 37°C while shaking. Bacteria CFU was then quantified by measuring optical density at 600 nm. For primary infections, bacterial culture was then diluted to 1x105 CFU/100 µL in sterile 1X PBS and 100 µL was injected per mouse. Both non-infected and infected mice were randomly assigned to a zero-dose sham (0 Gy) or irradiated (2 or 6 Gy) (Figure 1). We exposed mice to total body irradiation (TBI) in an acrylic, 12-slot mouse pie cage (MPC-1, Braintree Scientific, Braintree, MA) using a specimen turntable (XD1905-0000, Precision X-Ray Inc, Branford, CT). The mice were exposed to 0, 2, or 6 Gy X-ray IR (1.67 Gy/min; X-Rad 320, Precision X-Ray Inc.; filter, 0.75 mm tin/ 0.25 mm copper/1.5 mm aluminum).

Treatment ID:

TR004257

Treatment Summary:

All animal experiments were approved by the Georgetown University Institutional Animal Care and Use Committee (IACUC, protocol #2023-0012) and were conducted under all relevant federal and state guidelines. Male C57BL/6 mice (10 weeks old) were purchased from Charles River Laboratories (Frederick, MD) and provided food (PicoLab Rodent Diet 20 #5053) and deionized water was provided ad libitum. Mice were infected with a retro-orbital injection of Lm-OVA, which is a widely used and reproducible infection method as the bacteria can bypass the gut stage of infection. Lm-OVA stocks frozen at -80°C were grown overnight at 37°C while shaking in BHI broth supplemented with 5 µg/mL erythromycin. Then, overnight cultures were sub-cultured by diluting into fresh BHI broth supplemented with 5 µg/mL erythromycin and grown for 4 hours at 37°C while shaking. Bacteria CFU was then quantified by measuring optical density at 600 nm. For primary infections, bacterial culture was then diluted to 1x105 CFU/100 µL in sterile 1X PBS and 100 µL was injected per mouse. Both non-infected and infected mice were randomly assigned to a zero-dose sham (0 Gy) or irradiated (2 or 6 Gy) (Figure 1). We exposed mice to total body irradiation (TBI) in an acrylic, 12-slot mouse pie cage (MPC-1, Braintree Scientific, Braintree, MA) using a specimen turntable (XD1905-0000, Precision X-Ray Inc, Branford, CT). The mice were exposed to 0, 2, or 6 Gy X-ray IR (1.67 Gy/min; X-Rad 320, Precision X-Ray Inc.; filter, 0.75 mm tin/ 0.25 mm copper/1.5 mm aluminum).

Sample Preparation:

Sampleprep ID:	SP004254
Sampleprep Summary:	A 20 μL of urine was mixed with cold 50% acetonitrile (ACN) (80 μL) containing an internal standard (5 μM chlorpropamide [M+H]+ = 277.0414, [M-H]- = 275.0257). We prepared the samples on ice with vortexing and 10 min incubation periods following each step. Samples were then centrifuged at maximum speed for 10 min (10,000 x g, 4°C), with aliquots then being transferred to a liquid chromatography (LC) vial for analysis.

Sampleprep ID:

SP004254

Sampleprep Summary:

A 20 μL of urine was mixed with cold 50% acetonitrile (ACN) (80 μL) containing an internal standard (5 μM chlorpropamide [M+H]+ = 277.0414, [M-H]- = 275.0257). We prepared the samples on ice with vortexing and 10 min incubation periods following each step. Samples were then centrifuged at maximum speed for 10 min (10,000 x g, 4°C), with aliquots then being transferred to a liquid chromatography (LC) vial for analysis.

Combined analysis:

Analysis ID	AN006801	AN006802
Chromatography ID	CH005166	CH005166
MS ID	MS006500	MS006501
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Waters Acquity	Waters Acquity
Column	Waters ACQUITY UPLC BEH C18 (50 x 2.1 mm, 1.7 μm)	Waters ACQUITY UPLC BEH C18 (50 x 2.1 mm, 1.7 μm)
MS Type	ESI	ESI
MS instrument type	QTRAP	QTRAP
MS instrument name	Waters Xevo-G2-S	Waters Xevo-G2-S
Ion Mode	POSITIVE	NEGATIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH005166
Chromatography Summary:	The LC and MS conditions for serum was as follows: LC solvent A (water/0.1% formic acid [FA]), solvent B (acetonitrile/0.1% FA), and solvent C (isopropanol/0.1% FA). Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr. The gradient for serum was: 4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B at a flow rate of 0.5 mL/min, column temp 60°C.
Instrument Name:	Waters Acquity
Column Name:	Waters ACQUITY UPLC BEH C18 (50 x 2.1 mm, 1.7 μm)
Column Temperature:	60°C
Flow Gradient:	4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B
Flow Rate:	0.5 mL/min
Solvent A:	100% Water; 0.1% formic acid
Solvent B:	100% Acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase
Solvent C:	100% Isopropanol; 0.1% formic acid

MS:

MS ID:	MS006500
Analysis ID:	AN006801
Instrument Name:	Waters Xevo-G2-S
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr. The data are reported as normalized peak areas, normalized to all ions and internal std.
Ion Mode:	POSITIVE

MS ID:	MS006501
Analysis ID:	AN006802
Instrument Name:	Waters Xevo-G2-S
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr. The data are reported as normalized peak areas, normalized to all ions and internal std.
Ion Mode:	NEGATIVE