Summary of Study ST004100

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	ST004100
Study Title	Combined bacterial infection and radiation injury in the murine model: Consequences on metabolomics based biodosimetry (Serum 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:	SU004247
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
SA474594	674	Serum	1_NF_Sham	0Gy
SA474595	670	Serum	1_NF_Sham	0Gy
SA474596	669	Serum	1_NF_Sham	0Gy
SA474597	672	Serum	1_NF_Sham	0Gy
SA474598	673	Serum	1_NF_Sham	0Gy
SA474599	671	Serum	1_NF_Sham	0Gy
SA474600	675	Serum	2_NF_2Gy	2Gy
SA474601	676	Serum	2_NF_2Gy	2Gy
SA474602	677	Serum	2_NF_2Gy	2Gy
SA474603	678	Serum	2_NF_2Gy	2Gy
SA474604	679	Serum	2_NF_2Gy	2Gy
SA474605	680	Serum	2_NF_2Gy	2Gy
SA474606	685	Serum	3_NF_6Gy	6Gy
SA474607	686	Serum	3_NF_6Gy	6Gy
SA474608	684	Serum	3_NF_6Gy	6Gy
SA474609	683	Serum	3_NF_6Gy	6Gy
SA474610	682	Serum	3_NF_6Gy	6Gy
SA474611	681	Serum	3_NF_6Gy	6Gy
SA474612	720	Serum	4_Inf_Sham	0Gy
SA474613	719	Serum	4_Inf_Sham	0Gy
SA474614	718	Serum	4_Inf_Sham	0Gy
SA474615	716	Serum	4_Inf_Sham	0Gy
SA474616	715	Serum	4_Inf_Sham	0Gy
SA474617	713	Serum	5_Inf_2Gy	2Gy
SA474618	714	Serum	5_Inf_2Gy	2Gy
SA474619	709	Serum	5_Inf_2Gy	2Gy
SA474620	710	Serum	5_Inf_2Gy	2Gy
SA474621	711	Serum	5_Inf_2Gy	2Gy
SA474622	712	Serum	5_Inf_2Gy	2Gy
SA474623	704	Serum	6_Inf_6Gy	6Gy
SA474624	708	Serum	6_Inf_6Gy	6Gy
SA474625	707	Serum	6_Inf_6Gy	6Gy
SA474626	706	Serum	6_Inf_6Gy	6Gy
SA474627	705	Serum	6_Inf_6Gy	6Gy
SA474628	703	Serum	6_Inf_6Gy	6Gy
SA474629	701	Serum	6_Inf_6Gy	6Gy
SA474630	702	Serum	6_Inf_6Gy	6Gy

Showing results 1 to 37 of 37

Showing results 1 to 37 of 37

Collection:

Collection ID:	CO004240
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:	Blood (serum)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004256
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 subcultured 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:

TR004256

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 subcultured 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:	SP004253
Sampleprep Summary:	For serum, a 5 μl aliquot was mixed with 195 μl of cold 66% acetonitrile containing internal standards (5 μM chlorpropamide [M+H]+ = 277.0414, [M-H]- = 275.0257; deuterated amino acid mix). The deuterated amino acid mix contains 24 different labeled metabolites, ranging in concentration from 222 μM for glutamine-d5 to 7 μM for 1-methylhistidine-d3. The cold 66% acetonitrile used for metabolite extraction contained the amino acid mixture adjusted to a concentration of 10 μM for glutamine-d5. Samples were then prepared as above. One μl aliquots of each biofluid sample were combined as a quality control (QC) sample. Additional QC samples included the creatinine in frozen human urine and metabolites in frozen human plasma NIST Standard Reference Materials. The QC samples were injected every 10 samples along with blanks.

Sampleprep ID:

SP004253

Sampleprep Summary:

For serum, a 5 μl aliquot was mixed with 195 μl of cold 66% acetonitrile containing internal standards (5 μM chlorpropamide [M+H]+ = 277.0414, [M-H]- = 275.0257; deuterated amino acid mix). The deuterated amino acid mix contains 24 different labeled metabolites, ranging in concentration from 222 μM for glutamine-d5 to 7 μM for 1-methylhistidine-d3. The cold 66% acetonitrile used for metabolite extraction contained the amino acid mixture adjusted to a concentration of 10 μM for glutamine-d5. Samples were then prepared as above. One μl aliquots of each biofluid sample were combined as a quality control (QC) sample. Additional QC samples included the creatinine in frozen human urine and metabolites in frozen human plasma NIST Standard Reference Materials. The QC samples were injected every 10 samples along with blanks.

Combined analysis:

Analysis ID	AN006799	AN006800
Chromatography ID	CH005165	CH005165
MS ID	MS006498	MS006499
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Waters Acquity	Waters Acquity
Column	Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)
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:	CH005165
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 2.1mm,1.7um)
Column Temperature:	60
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:	MS006498
Analysis ID:	AN006799
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:	MS006499
Analysis ID:	AN006800
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