Summary of Study ST003459

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

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.

Study ID	ST003459
Study Title	Metabolomics of mice liver to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part5 mice liver 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 liver tissues from mice model revealed early septic biomarkers in liver.
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:	SU003587
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
SA382727	Blank_004	blank	Blank
SA382728	Blank_PB	blank	Blank
SA382729	Blank_001	blank	Blank
SA382730	Blank_002	blank	Blank
SA382731	Blank_003	blank	Blank
SA382698	SA021026	Liver	CLP (24h) / 12C-Serin
SA382699	SA020977	Liver	CLP (24h) / 12C-Serin
SA382700	SA020984	Liver	CLP (24h) / 12C-Serin
SA382701	SA021019	Liver	CLP (24h) / 12C-Serin
SA382702	SA020882	Liver	CLP (24h) / 13C-Serin
SA382703	SA020942	Liver	CLP (24h) / 13C-Serin
SA382704	SA020935	Liver	CLP (24h) / 13C-Serin
SA382705	SA020889	Liver	CLP (24h) / 13C-Serin
SA382706	SA020970	Liver	CLP (24h) / Vehicle
SA382707	SA020924	Liver	CLP (24h) / Vehicle
SA382708	SA020896	Liver	CLP (24h) / Vehicle
SA382709	QC_001	Liver	QC
SA382710	QC_009	Liver	QC
SA382711	QC_004	Liver	QC
SA382712	QC_008	Liver	QC
SA382713	QC_006	Liver	QC
SA382714	QC_007	Liver	QC
SA382715	QC_005	Liver	QC
SA382716	SA020991	Liver	Sham / 12C-Serin
SA382717	SA020998	Liver	Sham / 12C-Serin
SA382718	SA021012	Liver	Sham / 12C-Serin
SA382719	SA021005	Liver	Sham / 12C-Serin
SA382720	SA020910	Liver	Sham / 13C-Serin
SA382721	SA020903	Liver	Sham / 13C-Serin
SA382722	SA020963	Liver	Sham / 13C-Serin
SA382723	SA020956	Liver	Sham / 13C-Serin
SA382724	SA020949	Liver	Sham / Vehicle
SA382725	SA020917	Liver	Sham / Vehicle
SA382726	SA020929	Liver	Sham / Vehicle

Showing results 1 to 34 of 34

Showing results 1 to 34 of 34

Collection:

Collection ID:	CO003580
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:	Liver

Treatment:

Treatment ID:	TR003596
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:

TR003596

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:	SP003594
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:

SP003594

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.

Chromatography:

Chromatography ID:	CH004315
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

Analysis:

Analysis ID:	AN005683
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004315
Num Factors:	8
Num Metabolites:	106
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003459_AN005683_Results.txt
Units:	Normalized peak area

Analysis ID:	AN005684
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004315
Num Factors:	8
Num Metabolites:	48
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003459_AN005684_Results.txt
Units:	Normalized peak area