Summary of Study ST003456

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 IDST003456
Study TitleLipidomics of human serum to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part2 human lipids)
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 lipidome analysis of 151 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@hki-jena.de
Phone+4936415321265
Submit Date2024-08-28
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:SU003584
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
SA382049200731_213-Blankblank Blank NA
SA382050200724_004-Blank3blank Blank NA
SA382051200724_001-Blankblank Blank NA
SA382052200724_211-Blankblank Blank NA
SA382053200724_208-Blankblank Blank NA
SA382054200724_004-Blank_20200728103008blank Blank NA
SA382055200724_004-Blank2blank Blank NA
SA382056200724_002-Blankblank Blank NA
SA382057200724_002-Blank_20200728094839blank Blank NA
SA382058200724_004-Blankblank Blank NA
SA382059200724_001-Blank_20200728092738blank Blank NA
SA382060200731_420-Blankblank Blank NA
SA382061200731_214-Blankblank Blank NA
SA382062200731_216-Blankblank Blank NA
SA382063200808_426-Blankblank Blank NA
SA382064200808_425-Blankblank Blank NA
SA382065200808_575-Blankblank Blank NA
SA382066200808_428-Blankblank Blank NA
SA382067200808_578-Blank_20200812223120blank Blank NA
SA382068200808_578-Blank_20200810085413blank Blank NA
SA382069200731_423-Blankblank Blank NA
SA382070CS13095blood Control -1
SA382071CS13098blood Control -1
SA382072CS13149blood Control -1
SA382073CS13016blood Control -1
SA382074CS12989blood Control -1
SA382075CS13335blood Control -1
SA382076CS13254blood Control -1
SA382077CS13320blood Control -1
SA382078CS13101blood Control -1
SA382079CS12957blood Control -1
SA382080CS12954blood Control -1
SA382081CS13107blood Control -1
SA382082CS13239blood Control -1
SA382083CS12948blood Control -1
SA382084CS13089blood Control -1
SA382085CS13221blood Control -1
SA382086CS12981blood Control -1
SA382087CS13004blood Control -1
SA382088CS13113blood Control -1
SA382089CS13010blood Control -1
SA382090CS13013blood Control -1
SA382091CS13257blood Control -1
SA382092CS13019blood Control -1
SA382093CS13116blood Control -1
SA382094CS13164blood Control -1
SA382095CS13194blood Control -1
SA382096CS13001blood Control -1
SA382097CS13182blood Control -1
SA382098CS13218blood Control -1
SA382099CS13092blood Control -1
SA382100CS12951blood Control -1
SA382101CS13007blood Control -1
SA382102CS13104blood Control -1
SA382103CS13317blood Control -1
SA382104CS13110blood Control -1
SA382105CS13179blood Control -1
SA382106CS13215blood Control -1
SA382107CS13338blood Control -1
SA382108CS13178blood Control -2
SA382109CS13018blood Control -2
SA382110CS13181blood Control -2
SA382111CS13148blood Control -3
SA382112CS13334blood Control -3
SA382113CS13115blood Control -3
SA382114CS12980blood Control -3
SA382115CS13316blood Control -3
SA382116CS13015blood Control -3
SA382117CS13256blood Control -3
SA382118CS13003blood Control -3
SA382119CS13009blood Control -3
SA382120CS13000blood Control -3
SA382121CS13378blood Control -3
SA382122CS13094blood Control -3
SA382123CS13006blood Control -3
SA382124CS13088blood Control -3
SA382125CS13012blood Control -3
SA382126CS12950blood Control -3
SA382127CS13163blood Control -3
SA382128CS13238blood Control -3
SA382129CS13337blood Control -3
SA382130CS13253blood Control -3
SA382131CS13103blood Control -3
SA382132CS13319blood Control -3
SA382133CS13214blood Control -3
SA382134CS12953blood Control -3
SA382135CS13220blood Control -3
SA382136CS13100blood Control -3
SA382137CS13106blood Control -3
SA382138CS12947blood Control -3
SA382139CS13217blood Control -3
SA382140CS12956blood Control -3
SA382141CS13091blood Control -3
SA382142CS13193blood Control -3
SA382143CS13112blood Control -3
SA382144CS13097blood Control -3
SA382145CS13109blood Control -3
SA382146CS13011blood Control Pre
SA382147CS13096blood Control Pre
SA382148CS13318blood Control Pre
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Collection:

Collection ID:CO003577
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 lipidomic analysis.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003593
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 452 serum samples were retrieved from 151 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), 104 samples from 35 patients diagnosed with uncomplicated infection (UnInf), and 117 samples from 39 patients diagnosed with sepsis.

Sample Preparation:

Sampleprep ID:SP003591
Sampleprep Summary:For Lipidomics analysis, serum samples (10 μl) were transferred to a Spin-X® filter (0,22 µm, Costar) and diluted in a mixture of isopropanol, SPLASH® Lipidomix® (Avanti Polar Lipids) and butylated hydroxytoluene (90 μl, 96:4 vol/vol + 10 µg). The extract were then left at room temperature for 10 min before storage at -20°C over night. Samples were brought to room temperature and filtered by centrifugation (14 000 rpm, 5°C, 2 min). A aliquot (25 μl) was transferred into a high recovery HPLC vial and a equal parts mixture of mobile phase eluent A and B (75 µl) was added.

Combined analysis:

Analysis ID AN005677 AN005678
Chromatography ID CH004312 CH004312
MS ID MS005401 MS005402
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
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:CH004312
Methods Filename:Doneanu_etal.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:55°C
Flow Gradient:0-2 min: 40 % B, 2.1 min 50% B, 12 min 54% B, 12.1 min 70% B, 18-20 min 99 % B, 20.1-22 min 40% B
Flow Rate:0.4mL/min
Solvent A:60% Acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:90% Isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005401
Analysis ID:AN005677
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Peak areas were extracted using Compound Discoverer 3.0 (Thermo Scientific). Compound annotations were performed against the mzCloud (Thermo Scientific) MSMS library, the Human Metabolome Database 4.0 , and the MS-Omics lipid library covering 17 classes (CerP, DG, DGDG, Fatty acids, LysoPC, LysoPE, MG, PA, PC, PE, PG, PI, Plasmenyl-PC, Plasmenyl-PE, PS, SM and TG). 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 3 ppm), and MS/MS spectra, Level 2a: identification by retention times (compared against in-house authentic standards and lipid class behaviour), accurate mass (with an accepted deviation of 3ppm). Level 2b: identification by accurate mass (with an accepted deviation of 3 ppm), and MS/MS spectra, Level 3: identification by accurate mass alone (with an accepted deviation of 3 ppm). Lipid annotations were curated manually by comparing retention time behaviour over the number of tail chain carbons and double bonds as annotated. 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:MS005402
Analysis ID:AN005678
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Peak areas were extracted using Compound Discoverer 3.0 (Thermo Scientific). Compound annotations were performed against the mzCloud (Thermo Scientific) MSMS library, the Human Metabolome Database 4.0 , and the MS-Omics lipid library covering 17 classes (CerP, DG, DGDG, Fatty acids, LysoPC, LysoPE, MG, PA, PC, PE, PG, PI, Plasmenyl-PC, Plasmenyl-PE, PS, SM and TG). 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 3 ppm), and MS/MS spectra, Level 2a: identification by retention times (compared against in-house authentic standards and lipid class behaviour), accurate mass (with an accepted deviation of 3ppm). Level 2b: identification by accurate mass (with an accepted deviation of 3 ppm), and MS/MS spectra, Level 3: identification by accurate mass alone (with an accepted deviation of 3 ppm). Lipid annotations were curated manually by comparing retention time behaviour over the number of tail chain carbons and double bonds as annotated. 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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