Summary of Study ST003461

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 PR002122. The data can be accessed directly via it's Project DOI: 10.21228/M8B52G This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST003461
Study Title	Metabolomics of mice spleen to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part7 mice spleen metabolite)
Study Summary	Sepsis, a life-threatening organ dysfunction caused by a dysregulated response to infection, is a critical medical condition with significant global impact, responsible for 48.9 million cases and 11 million deaths annually. Metabolic dysregulation in sepsis is a critical determinant of disease outcome, yet most studies focus on patients after severe illness onset, comparing septic versus non-septic groups or survivors versus non-survivors. To truly understand this complex disease, it is essential to investigate early metabolic shifts, capturing the transition from simple infection to sepsis. Our untargeted metabolome analysis of spleen tissues from mice model revealed early septic biomarkers in spleen.
Institute	Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
Department	Microbiome Dynamics
Last Name	XU
First Name	LINLIN
Address	Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Email	Lin-Lin.Xu@hki-jena.de
Phone	+4936415321265
Submit Date	2024-09-04
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-05-26
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002122
Project DOI:	doi: 10.21228/M8B52G
Project Title:	Early Metabolic Shifts in the Sepsis: Insights from Presymptomatic Patients and In Vivo Models.
Project Type:	MS quantitative analysis
Project Summary:	Metabolomics of human serum to support understanding of early metabolic shift in presymptomatic sepsis patients and further confirmed in in vivo model.
Institute:	Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
Department:	Microbiome Dynamics
Last Name:	XU
First Name:	LINLIN
Address:	Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Email:	Lin-Lin.Xu@leibniz-hki.de
Phone:	+4936415321265

Subject:

Subject ID:	SU003589
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Sample source	Group
SA382794	Blank_PB	blank	Blank
SA382795	Blank_001	blank	Blank
SA382796	Blank_002	blank	Blank
SA382797	Blank_003	blank	Blank
SA382798	Blank_004	blank	Blank
SA382765	SA020978	Spleen	CLP (24h) / 12C-Serin
SA382766	SA021020	Spleen	CLP (24h) / 12C-Serin
SA382767	SA021027	Spleen	CLP (24h) / 12C-Serin
SA382768	SA020985	Spleen	CLP (24h) / 12C-Serin
SA382769	SA020936	Spleen	CLP (24h) / 13C-Serin
SA382770	SA020890	Spleen	CLP (24h) / 13C-Serin
SA382771	SA020883	Spleen	CLP (24h) / 13C-Serin
SA382772	SA020943	Spleen	CLP (24h) / 13C-Serin
SA382773	SA020897	Spleen	CLP (24h) / Vehicle
SA382774	SA020971	Spleen	CLP (24h) / Vehicle
SA382775	SA020925	Spleen	CLP (24h) / Vehicle
SA382776	QC_001	Spleen	QC
SA382777	QC_009	Spleen	QC
SA382778	QC_004	Spleen	QC
SA382779	QC_008	Spleen	QC
SA382780	QC_006	Spleen	QC
SA382781	QC_007	Spleen	QC
SA382782	QC_005	Spleen	QC
SA382783	SA021006	Spleen	Sham / 12C-Serin
SA382784	SA021013	Spleen	Sham / 12C-Serin
SA382785	SA020999	Spleen	Sham / 12C-Serin
SA382786	SA020992	Spleen	Sham / 12C-Serin
SA382787	SA020964	Spleen	Sham / 13C-Serin
SA382788	SA020911	Spleen	Sham / 13C-Serin
SA382789	SA020904	Spleen	Sham / 13C-Serin
SA382790	SA020957	Spleen	Sham / 13C-Serin
SA382791	SA020930	Spleen	Sham / Vehicle
SA382792	SA020918	Spleen	Sham / Vehicle
SA382793	SA020950	Spleen	Sham / Vehicle

Showing results 1 to 34 of 34

Showing results 1 to 34 of 34

Collection:

Collection ID:	CO003582
Collection Summary:	Mice tissue samples were collected from our in vivo mice model and frozen at -80 °C. Samples were shipped to MS-OMICS for metabolomic analysis.
Sample Type:	Spleen

Treatment:

Treatment ID:	TR003598
Treatment Summary:	Approximately 30% of the cecum was ligated and punctured twice with a 23 Gauge (G) needle. A small amount of faeces was extruded and the cecum was placed back into the abdominal cavity. All animals received 40 mL/kg saline s.c. directly after the procedure and once 25mg/kg s.c. Imipenem/Cilastatin after 6 hours. This model is associated with a 14-day mortality of 30%, closely mimicking the clinical situation. Animals were orally gavaged with 500mg/kg 12C-Serin (Sigma) or 13C-Serin (CLM-1574-H-0.25 Serine-L (13C3 99%13C), Euroisotope, Germany) in 10mL/kg drinking water or drinking water only (vehicle) 6 and 18 hours after CLP98,99. After 24 hours, the animals are then perfused with ice cold PBS and organs were harvested, snap frozen and stored at -80° until further analysis. Sham animals underwent exactly to the same procedures except for the CLP.

Treatment ID:

TR003598

Treatment Summary:

Approximately 30% of the cecum was ligated and punctured twice with a 23 Gauge (G) needle. A small amount of faeces was extruded and the cecum was placed back into the abdominal cavity. All animals received 40 mL/kg saline s.c. directly after the procedure and once 25mg/kg s.c. Imipenem/Cilastatin after 6 hours. This model is associated with a 14-day mortality of 30%, closely mimicking the clinical situation. Animals were orally gavaged with 500mg/kg 12C-Serin (Sigma) or 13C-Serin (CLM-1574-H-0.25 Serine-L (13C3 99%13C), Euroisotope, Germany) in 10mL/kg drinking water or drinking water only (vehicle) 6 and 18 hours after CLP98,99. After 24 hours, the animals are then perfused with ice cold PBS and organs were harvested, snap frozen and stored at -80° until further analysis. Sham animals underwent exactly to the same procedures except for the CLP.

Sample Preparation:

Sampleprep ID:	SP003596
Sampleprep Summary:	To prepare samples for semi-polar metabolites extraction, the different tissue samples were weighted and transferred to Eppendorf tubes. Ceramic beads and precooled methanol/water (1:2) were added. All tubes were placed in a pre-cooled (-20°C) bead beater and homogenized (4 x 30 sec., 30 Hz) followed by ultrasonication (5 min). After centrifugation (18000 RCF, 5 min, 4°C), the supernatant was collected. The sample pellet was reextracted as described above. The two extract supernatants were pooled and passed through a phosphor removal cartridge (Phree filter plates). A precise aliquot of the extract was evaporated to dryness under a gentle stream of nitrogen, before reconstitution with 10% Eluent B in Eluent A. All Samples were diluted 5 times in mobile phase eluent A and stable isotope labelled standards were added before analysis. Mouse serum (50 μl) was diluted with a mixture of acetonitrile and methanol (200 μl 1:1 v/v). The extract was then passed through a phosphor removal cartridge (Phree, Phenomenex). An aliquot (100 μl) was transferred into a high recovery HPLC vial and the solvent was removed under a gentle flow of nitrogen. Extracts were reconstituted in a mobile phase mixture (100 μl, 10%B in 90%A). To ensure high-quality sample preparation, a quality control sample (QC sample) was prepared by pooling small equal aliquots from each sample, to create a representative average of the entire set.

Sampleprep ID:

SP003596

Sampleprep Summary:

To prepare samples for semi-polar metabolites extraction, the different tissue samples were weighted and transferred to Eppendorf tubes. Ceramic beads and precooled methanol/water (1:2) were added. All tubes were placed in a pre-cooled (-20°C) bead beater and homogenized (4 x 30 sec., 30 Hz) followed by ultrasonication (5 min). After centrifugation (18000 RCF, 5 min, 4°C), the supernatant was collected. The sample pellet was reextracted as described above. The two extract supernatants were pooled and passed through a phosphor removal cartridge (Phree filter plates). A precise aliquot of the extract was evaporated to dryness under a gentle stream of nitrogen, before reconstitution with 10% Eluent B in Eluent A. All Samples were diluted 5 times in mobile phase eluent A and stable isotope labelled standards were added before analysis. Mouse serum (50 μl) was diluted with a mixture of acetonitrile and methanol (200 μl 1:1 v/v). The extract was then passed through a phosphor removal cartridge (Phree, Phenomenex). An aliquot (100 μl) was transferred into a high recovery HPLC vial and the solvent was removed under a gentle flow of nitrogen. Extracts were reconstituted in a mobile phase mixture (100 μl, 10%B in 90%A). To ensure high-quality sample preparation, a quality control sample (QC sample) was prepared by pooling small equal aliquots from each sample, to create a representative average of the entire set.

Combined analysis:

Analysis ID	AN005687	AN005688
Chromatography ID	CH004317	CH004317
MS ID	MS005411	MS005412
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap Exploris 240	Thermo Orbitrap Exploris 240
Ion Mode	POSITIVE	NEGATIVE
Units	Normalized peak area	Normalized peak area

Chromatography:

Chromatography ID:	CH004317
Methods Filename:	Doneanu_etal.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:	30
Flow Gradient:	0-2 min: 0 % B, 4 min 35% B, 6-14 min 90% B, 14.1-15 min 0% B.
Flow Rate:	0.3mL/min
Solvent A:	100% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:	100% methanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005411
Analysis ID:	AN005687
Instrument Name:	Thermo Orbitrap Exploris 240
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Semi-polar metabolite profiling was performed by MS-Omics (Vedbæk, Denmark). The analysis was carried out using a Vanquish LC (Thermo Scientific) coupled to a Orbitrap Exploris 240 MS (Thermo Scientific). The UHPLC was performed using an adapted version of the protocol described by Doneanu et al . An electrospray ionization interface was used as ionization source. Analysis was performed in positive and negative ionization mode under polarity switching. Metabolomics processing was performed untargeted using Compound Discoverer 3.3 (Thermo Scientific) and Skyline 22.2 (MacCoss Lab Software) for peak picking and feature grouping, followed by an in-house annotation and curation pipeline written in MatLab (2022b, MathWorks). Identification of compounds were performed at four levels; Level 1: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 2a: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm). Level 2b: identification by accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 3: identification by accurate mass alone (with an accepted deviation of 3ppm). The data have been normalized to the QC samples to remove systematic drift over the analysis sequence. The normalization is performed using linear regression for the QC’s within each analytical batch with signal = ainjection number – b. Each value is then normalized with: normSignal = average(all QC samples)(signal – injection number*a)/b. This is done independently for each compound.
Ion Mode:	POSITIVE
Analysis Protocol File:	Doneanu_etal.pdf

MS ID:	MS005412
Analysis ID:	AN005688
Instrument Name:	Thermo Orbitrap Exploris 240
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Semi-polar metabolite profiling was performed by MS-Omics (Vedbæk, Denmark). The analysis was carried out using a Vanquish LC (Thermo Scientific) coupled to a Orbitrap Exploris 240 MS (Thermo Scientific). The UHPLC was performed using an adapted version of the protocol described by Doneanu et al . An electrospray ionization interface was used as ionization source. Analysis was performed in positive and negative ionization mode under polarity switching. Metabolomics processing was performed untargeted using Compound Discoverer 3.3 (Thermo Scientific) and Skyline 22.2 (MacCoss Lab Software) for peak picking and feature grouping, followed by an in-house annotation and curation pipeline written in MatLab (2022b, MathWorks). Identification of compounds were performed at four levels; Level 1: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 2a: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm). Level 2b: identification by accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 3: identification by accurate mass alone (with an accepted deviation of 3ppm). The data have been normalized to the QC samples to remove systematic drift over the analysis sequence. The normalization is performed using linear regression for the QC’s within each analytical batch with signal = ainjection number – b. Each value is then normalized with: normSignal = average(all QC samples)(signal – injection number*a)/b. This is done independently for each compound.
Ion Mode:	NEGATIVE
Analysis Protocol File:	Doneanu_etal.pdf