Summary of Study ST000920

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 PR000636. The data can be accessed directly via it's Project DOI: 10.21228/M8G39P 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.

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Study IDST000920
Study TitleDiscovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics
Study TypeUntargeted lipidomics
Study SummaryTraumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative ion modes by Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection,. Polyunsaturated fatty acids (PUFAs) and PUFA-containing diacylglycerols were found to be upregulated in sera from injured rats, while changes in sphingolipids and other membrane phospholipids were also observed, many of which map to known secondary injury pathways. Overall, the identified biomarker panel offers viable molecular candidates representing lipids that may readily cross the blood brain barrier (BBB) and aid in the understanding of TBI pathophysiology.
Institute
Georgia Institute of Technology
DepartmentChemistry
LaboratoryFernández
Last NameHogan
First NameScott
Address311 Ferst Dr
Emailsrjhogan@gatech.edu
Phone2156924657
Submit Date2018-01-19
Num Groups5
Total Subjects34
Num Males34
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2018-04-10
Release Version1
Scott Hogan Scott Hogan
https://dx.doi.org/10.21228/M8G39P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000636
Project DOI:doi: 10.21228/M8G39P
Project Title:Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics
Project Type:Untargeted Lipidomics
Project Summary:Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative ion modes by Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection,. Polyunsaturated fatty acids (PUFAs) and PUFA-containing diacylglycerols were found to be upregulated in sera from injured rats, while changes in sphingolipids and other membrane phospholipids were also observed, many of which map to known secondary injury pathways. Overall, the identified biomarker panel offers viable molecular candidates representing lipids that may readily cross the blood brain barrier (BBB) and aid in the understanding of TBI pathophysiology.
Institute:Georgia Institute of Technology
Department:Chemistry
Laboratory:Fernández
Last Name:Hogan
First Name:Scott
Address:901 Atlantic Drive, Atlanta, GA, 30332, USA
Email:srjhogan@gatech.edu
Phone:2156924657

Subject:

Subject ID:SU000958
Subject Type:Rat
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Genotype Strain:Sprague-dawley
Age Or Age Range:8 weeks
Weight Or Weight Range:300-400 g
Gender:male

Factors:

Subject type: Rat; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Class
SA054636NA5naïve
SA054637NA1naïve
SA054638NA7naïve
SA054639NA8naïve
SA054640NA2naïve
SA054641NA6naïve
SA054642NA4naïve
SA054643NA3naïve
SA054644NA0naïve
SA054645NA9naïve
SA054612SA7SHAM
SA054613SA3SHAM
SA054614SC7SHAM
SA054615SB3SHAM
SA054616SD7SHAM
SA054617SC3SHAM
SA054618SD3SHAM
SA054619SB7SHAM
SA054620TM3TBI
SA054621TC7TBI
SA054622TP3TBI
SA054623TJ3TBI
SA054624TK3TBI
SA054625TE7TBI
SA054626TI7TBI
SA054627TN3TBI
SA054628TL3TBI
SA054629TG7TBI
SA054630TF7TBI
SA054631TB7TBI
SA054632TD7TBI
SA054633TA7TBI
SA054634TO3TBI
SA054635TH7TBI
Showing results 1 to 34 of 34

Collection:

Collection ID:CO000952
Collection Summary:During the afternoon, approximately 200 µL of whole blood was collected from a tail vein punctured by 20-gauge Precision Glide needles (Beckton Dickinson) and stored on ice. Whole blood samples were allowed to coagulate at room temperature for 45 minutes, and all sample collection followed literature guidelines for limiting the potential for hemolysis.37-39 Samples were then centrifuged at 4 °C for 15 min at 2500 x g, and serum was collected in 50 μL aliquots and stored at -80 °C.
Sample Type:Serum

Treatment:

Treatment ID:TR000972
Treatment Summary:Unilateral contusions of the lateral frontoparietal cortex were created using a controlled cortical impact (CCI) device (Pittsburgh Precision Instruments, Pittsburgh, PA) following published procedures. Rats were anesthetized (induction, 5% isoflurane; maintenance 2-3% isoflurane), mounted in a stereotaxic frame and a 6 mm craniectomy was made over the left frontoparietal cortex (center: -3.0 mm AP, +2.0 mm ML from bregma). A pneumatic piston (tip diameter=5 mm; positioned 15 degrees from vertical in the coronal plane) impacted the cortical tissue to a depth of 2 mm (velocity=4 m/s, duration=200 ms), values consistent with a moderate TBI insult

Sample Preparation:

Sampleprep ID:SP000965
Sampleprep Summary:Prior to analysis, lipids and small non-polar metabolites were separated from proteins in blood using isopropyl alcohol (IPA) for protein precipitation, shown to be advantageous over the Folch or Bligh and Dyer methods for a variety of experimental considerations.40-42 For protein precipitation purposes, serum samples were thawed on ice for 1 h and serum was mixed 1:3 v/v with IPA. Samples were centrifuged at 16,000 x g for 7 min, and the supernatant was collected. Samples were stored at -80 °C until analysis.

Combined analysis:

Analysis ID AN001508 AN001509
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity H-Class Waters Acquity H-Class
Column Waters ACQUITY UPLC BEH C18 Waters ACQUITY UPLC BEH C18
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE NEGATIVE
Units normalized abundance normalized abundance

Chromatography:

Chromatography ID:CH001063
Instrument Name:Waters Acquity H-Class
Column Name:Waters ACQUITY UPLC BEH C18
Column Temperature:60° C
Flow Rate:.3 mL/min
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:10% acetonitrile/90% isopropanol; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS001391
Analysis ID:AN001508
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3.0 kV
Source Temperature:80° C
Desolvation Gas Flow:600 L/h
Desolvation Temperature:150° C
  
MS ID:MS001392
Analysis ID:AN001509
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:-2.3 kV
Source Temperature:90° C
Desolvation Gas Flow:600 L/h
Desolvation Temperature:250° C
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