Summary of Study ST003439

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

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Study IDST003439
Study TitleMetabolomics of human serum to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part1 human metabolites)
Study SummarySepsis, 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 serum metabolome analysis of 152 presymptomatic patients undergoing major elective surgery revealed early metabolic signals in sepsis.
Institute
Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
DepartmentMicrobiome Dynamics
Last NameXu
First NameLinlin
AddressBeutenbergstraße 11a, Jena, Thuringia, 07745, Germany
EmailLin-Lin.Xu@leibniz-hki.de
Phone+4936415321265
Submit Date2024-08-14
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-05-26
Release Version1
Linlin Xu Linlin Xu
https://dx.doi.org/10.21228/M8B52G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU003580
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:63 (21, 80)
Gender:Male and female
Species Group:Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Group Timepoint
SA380974200802_217-Blankblank Blank NA
SA380975200724_001-Blankblank Blank NA
SA380976200724_002-Blankblank Blank NA
SA380977200724_006-Blankblank Blank NA
SA380978200724_215-Blankblank Blank NA
SA380979200730_217-Blankblank Blank NA
SA380980200730_218-Blankblank Blank NA
SA380981200730_222-Blankblank Blank NA
SA380982200730_426-Blankblank Blank NA
SA380983200730_431-Blankblank Blank NA
SA380984200730_217-Blank_20200730112558blank Blank NA
SA380985200724_210-Blankblank Blank NA
SA380986200802_218-Blankblank Blank NA
SA380987200803_218-SystemBlank2blank Blank NA
SA380988200807_433-Blankblank Blank NA
SA380989200807_434-Blankblank Blank NA
SA380990200807_438-Blankblank Blank NA
SA380991200807_585-Blankblank Blank NA
SA380992200807_590-Blankblank Blank NA
SA380993200803_217-SystemBlank2blank Blank NA
SA380994CS12957blood Control -1
SA380995CS13116blood Control -1
SA380996CS12989blood Control -1
SA380997CS13007blood Control -1
SA380998CS13320blood Control -1
SA380999CS13019blood Control -1
SA381000CS12948blood Control -1
SA381001CS13221blood Control -1
SA381002CS13257blood Control -1
SA381003CS13004blood Control -1
SA381004CS13089blood Control -1
SA381005CS13110blood Control -1
SA381006CS13010blood Control -1
SA381007CS12981blood Control -1
SA381008CS13182blood Control -1
SA381009CS13239blood Control -1
SA381010CS13149blood Control -1
SA381011CS13254blood Control -1
SA381012CS13098blood Control -1
SA381013CS13335blood Control -1
SA381014CS13101blood Control -1
SA381015CS13338blood Control -1
SA381016CS13016blood Control -1
SA381017CS12951blood Control -1
SA381018CS13218blood Control -1
SA381019CS13107blood Control -1
SA381020CS13194blood Control -1
SA381021CS13095blood Control -1
SA381022CS13092blood Control -1
SA381023CS13164blood Control -1
SA381024CS12954blood Control -1
SA381025CS13013blood Control -1
SA381026CS13179blood Control -1
SA381027CS13113blood Control -1
SA381028CS13001blood Control -1
SA381029CS13317blood Control -1
SA381030CS13104blood Control -1
SA381031CS13215blood Control -1
SA381032CS13181blood Control -2
SA381033CS13178blood Control -2
SA381034CS13018blood Control -2
SA381035CS13106blood Control -3
SA381036CS13100blood Control -3
SA381037CS13253blood Control -3
SA381038CS13214blood Control -3
SA381039CS13006blood Control -3
SA381040CS12953blood Control -3
SA381041CS13091blood Control -3
SA381042CS13378blood Control -3
SA381043CS12980blood Control -3
SA381044CS13115blood Control -3
SA381045CS13337blood Control -3
SA381046CS13015blood Control -3
SA381047CS12947blood Control -3
SA381048CS13148blood Control -3
SA381049CS13109blood Control -3
SA381050CS13097blood Control -3
SA381051CS13220blood Control -3
SA381052CS13000blood Control -3
SA381053CS13316blood Control -3
SA381054CS13217blood Control -3
SA381055CS13256blood Control -3
SA381056CS13163blood Control -3
SA381057CS13319blood Control -3
SA381058CS12956blood Control -3
SA381059CS13012blood Control -3
SA381060CS13112blood Control -3
SA381061CS13003blood Control -3
SA381062CS13094blood Control -3
SA381063CS13009blood Control -3
SA381064CS13193blood Control -3
SA381065CS13103blood Control -3
SA381066CS13088blood Control -3
SA381067CS13334blood Control -3
SA381068CS13238blood Control -3
SA381069CS12950blood Control -3
SA381070CS13162blood Control Pre
SA381071CS13093blood Control Pre
SA381072CS13090blood Control Pre
SA381073CS13105blood Control Pre
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Collection:

Collection ID:CO003573
Collection Summary:Human serum samples were collected from presymptomatic sepsis patients scheduled for elective surgery before operation and up to one day before diagnosis, matched with uncomplicated infection and healthy controls and frozen at -80 °C. Samples were shipped to MS-OMICS for metabolomic analysis.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003589
Treatment Summary:we retrieved samples from patients scheduled for elective surgery, corresponding to time point Pre (pre-operation), -3, -2 and -1 days before the clinical diagnosis. A total of 455 serum samples were retrieved from 152 patients, including 114 samples from 38 non-infected patients making an uncomplicated postoperative recovery (referred to as Control), 117 samples from 39 patients developing a systemic inflammatory response (SIRS), 107 samples from 36 patients diagnosed with uncomplicated infection (UnInf), and 117 samples from 39 patients diagnosed with sepsis.

Sample Preparation:

Sampleprep ID:SP003587
Sampleprep Summary:For semi-polar metabolite analysis, serum samples (50 μl) were diluted with a mixture of acetonitrile, methanol, formic acid and stable isotope labelled internal standards (200 μl 1.00:0.99:0.01 v/ v/ v). The extracts were then passed through a phosphor lipid removal cartridge (Phree, Phenomenex) using centrifugation (1 400 rpm, 4°C, 10 min). 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 reverse phase mobile phase mixture (100 μl, 10% B in 90% A).

Combined analysis:

Analysis ID AN005670 AN005671
Chromatography ID CH004306 CH004306
MS ID MS005394 MS005395
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 Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Normalized peak area Normalized peak area

Chromatography:

Chromatography ID:CH004306
Chromatography Summary:Sample analysis was carried out by MS-Omics. The UHPLC was performed using a adapted version of the protocol described by Doneanu et al(UPLC/MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes, Water Application note 2011, 720004042en). The analysis was carried out using a Thermo Scientific Vanquish LC coupled to a Q Exactive™ HF Hybrid Quadrupole-Orbitrap, Thermo Fisher Scientific.
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:MS005394
Analysis ID:AN005670
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolomics processing was performed untargeted using Compound Discoverer 3.0 (Thermo Scientific) for peak picking and feature grouping, followed by a in-house annotation and curation pipeline written in MatLab (2021b, 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 = a*injection 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:MS005395
Analysis ID:AN005671
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolomics processing was performed untargeted using Compound Discoverer 3.0 (Thermo Scientific) for peak picking and feature grouping, followed by a in-house annotation and curation pipeline written in MatLab (2021b, 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 = a*injection 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
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