Summary of Study ST001950

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 PR001237. The data can be accessed directly via it's Project DOI: 10.21228/M8TB0S This work is supported by NIH grant, U2C- DK119886.

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Study IDST001950
Study TitleLipidome Alterations Following Mild Traumatic Brain Injury.
Study TypeUntargeted Lipidomics
Study SummaryTraumatic brain injury (TBI) poses a major health challenge, with tens of millions of new cases reported globally every year. Brain damage resulting from TBI can vary significantly due to factors including injury severity, diffusivity, modality, time delay relative to impact, and exposure to repeated injury events. Untargeted lipidomic analysis of Sprague-Dawley rat serum within 24 hours of mild single and repeat controlled cortical impact (CCI) injury events led to the discovery of biomarker candidates of TBI. Lipid biomarkers have a unique potential to serve as objective molecular measures of the body’s response to injury as their alteration in brain tissue can be more freely observed than for larger protein markers. Animal serum was analyzed via ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in positive and negative ion modes. Known lipid species were identified through matching to in-house tandem MS databases. Machine learning and feature selection approaches were used to construct lipid panels capable of distinguishing serum from injured and uninjured animals across a range of injury severities and timepoints within the first day of injury. The best multivariate lipid panels had over 90% cross-validated sensitivity, selectivity, and accuracy and consisted of species from nine different lipid classes. These mapped onto sphingolipid signaling, autophagy, necroptosis and glycerophospholipid metabolism pathways, with FDR corrected p-values better than 0.05.
Institute
Georgia Institute of Technology
DepartmentChemistry and Biochemistry
LaboratoryFacundo Fernández
Last NameGier
First NameEric
Address311 Ferst Drive, Atlanta, GA, 30318, USA
Emailegier3@gatech.edu
Phone2246221699
Submit Date2021-10-24
Num Groups6
Total Subjects32
Num Males14
Num Females18
Study CommentsLC-MS
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-02-07
Release Version1
Eric Gier Eric Gier
https://dx.doi.org/10.21228/M8TB0S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001237
Project DOI:doi: 10.21228/M8TB0S
Project Title:Lipidome Alterations Following Mild Traumatic Brain Injury.
Project Summary:Traumatic brain injury (TBI) poses a major health challenge, with tens of millions of new cases reported globally every year. Brain damage resulting from TBI can vary significantly due to factors including injury severity, diffusivity, modality, time delay relative to impact, and exposure to repeated injury events. Untargeted lipidomic analysis of Sprague-Dawley rat serum within 24 hours of mild single and repeat controlled cortical impact (CCI) injury events led to the discovery of biomarker candidates of TBI. Lipid biomarkers have a unique potential to serve as objective molecular measures of the body’s response to injury as their alteration in brain tissue can be more freely observed than for larger protein markers. Animal serum was analyzed via ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in positive and negative ion modes. Known lipid species were identified through matching to in-house tandem MS databases. Machine learning and feature selection approaches were used to construct lipid panels capable of distinguishing serum from injured and uninjured animals across a range of injury severities and timepoints within the first day of injury. The best multivariate lipid panels had over 90% cross-validated sensitivity, selectivity, and accuracy and consisted of species from nine different lipid classes. These mapped onto sphingolipid signaling, autophagy, necroptosis and glycerophospholipid metabolism pathways, with FDR corrected p-values better than 0.05.
Institute:Georgia Institute of Technology
Department:Chemistry and Biochemistry
Laboratory:Facundo Fernández
Last Name:Gier
First Name:Eric
Address:311 Ferst Dr. Atlanta, GA, 30318, USA
Email:ericgier4@gmail.com
Phone:2246221699

Subject:

Subject ID:SU002028
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Genotype Strain:Sprague-Dawley
Age Or Age Range:8 weeks
Weight Or Weight Range:250-450 g
Gender:Male and female
Animal Animal Supplier:Charles River
Animal Light Cycle:12 h reverse light-dark cycles
Animal Feed:ad libitum
Animal Water:ad libitum

Factors:

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

mb_sample_id local_sample_id Injury Severity Sex Blood Collection
SA18392428D_T4_I3_G1_L1Repeat-Impact F 24 hour
SA18392520D_T4_I3_G1_L1Repeat-Impact F 24 hour
SA18392630D_T4_I3_G1_L1Repeat-Impact F 24 hour
SA18392732D_T4_I3_G1_L1Repeat-Impact F 24 hour
SA18392823D_T4_I3_G1_L1Repeat-Impact F 24 hour
SA18392924B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393023B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393116B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393228B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393332B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393420B_T2_I3_G1_L1Repeat-Impact F 30 min
SA18393520C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18393630B_T2_I3_G1_L1Repeat-Impact F 4 hour
SA18393728C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18393816C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18393930C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18394023C_T3_I3_G1_L2Repeat-Impact F 4 hour
SA18394132C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18394224C_T3_I3_G1_L1Repeat-Impact F 4 hour
SA18394330A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394432A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394523A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394620A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394716A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394824A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18394928A_T1_I3_G1_L1Repeat-Impact F Baseline
SA18395011D_T4_I3_G2_L1Repeat-Impact M 24 hour
SA1839519D_T4_I3_G2_L1Repeat-Impact M 24 hour
SA18395212D_T4_I3_G2_L1Repeat-Impact M 24 hour
SA1839534D_T4_I3_G2_L1Repeat-Impact M 24 hour
SA18395411B_T2_I3_G2_L1Repeat-Impact M 30 min
SA18395512B_T2_I3_G2_L1Repeat-Impact M 30 min
SA18395612C_T3_I3_G2_L1Repeat-Impact M 4 hour
SA18395711C_T3_I3_G2_L1Repeat-Impact M 4 hour
SA1839584C_T3_I3_G2_L1Repeat-Impact M 4 hour
SA1839599C_T3_I3_G2_L1Repeat-Impact M 4 hour
SA1839609A_T1_I3_G2_L1Repeat-Impact M Baseline
SA18396111A_T1_I3_G2_L1Repeat-Impact M Baseline
SA18396212A_T1_I3_G2_L1Repeat-Impact M Baseline
SA1839634A_T1_I3_G2_L1Repeat-Impact M Baseline
SA18396418D_T4_I1_G1_L1Sham F 24 hour
SA18396521D_T4_I1_G1_L1Sham F 24 hour
SA18396631D_T4_I1_G1_L1Sham F 24 hour
SA18396719D_T4_I1_G1_L1Sham F 24 hour
SA18396814D_T4_I1_G1_L1Sham F 24 hour
SA18396931B_T2_I1_G1_L1Sham F 30 min
SA18397018B_T2_I1_G1_L1Sham F 30 min
SA18397119B_T2_I1_G1_L2Sham F 30 min
SA18397214B_T2_I1_G1_L1Sham F 30 min
SA18397331C_T3_I1_G1_L1Sham F 4 hour
SA18397421C_T3_I1_G1_L2Sham F 4 hour
SA18397518C_T3_I1_G1_L1Sham F 4 hour
SA18397614C_T3_I1_G1_L1Sham F 4 hour
SA18397719C_T3_I1_G1_L1Sham F 4 hour
SA18397818A_T1_I1_G1_L1Sham F Baseline
SA18397914A_T1_I1_G1_L1Sham F Baseline
SA18398031A_T1_I1_G1_L1Sham F Baseline
SA18398125D_T4_I1_G2_L1Sham M 24 hour
SA1839822D_T4_I1_G2_L1Sham M 24 hour
SA1839831D_T4_I1_G2_L1Sham M 24 hour
SA1839847D_T4_I1_G2_L1Sham M 24 hour
SA1839855D_T4_I1_G2_L1Sham M 24 hour
SA18398626D_T4_I1_G2_L1Sham M 24 hour
SA1839877B_T2_I1_G2_L1Sham M 30 min
SA18398825B_T2_I1_G2_L1Sham M 30 min
SA18398926B_T2_I1_G2_L1Sham M 30 min
SA1839905B_T2_I1_G2_L1Sham M 30 min
SA1839912B_T2_I1_G2_L1Sham M 30 min
SA1839921C_T3_I1_G2_L1Sham M 4 hour
SA1839932C_T3_I1_G2_L1Sham M 4 hour
SA1839945C_T3_I1_G2_L1Sham M 4 hour
SA1839957C_T3_I1_G2_L1Sham M 4 hour
SA18399625C_T3_I1_G2_L1Sham M 4 hour
SA18399726C_T3_I1_G2_L1Sham M 4 hour
SA18399826A_T1_I1_G2_L1Sham M Baseline
SA1839995A_T1_I1_G2_L1Sham M Baseline
SA1840002A_T1_I1_G2_L1Sham M Baseline
SA18400125A_T1_I1_G2_L1Sham M Baseline
SA1840027A_T1_I1_G2_L1Sham M Baseline
SA18400327D_T4_I2_G1_L1Single-Impact F 24 hour
SA18400422D_T4_I2_G1_L1Single-Impact F 24 hour
SA18400517D_T4_I2_G1_L1Single-Impact F 24 hour
SA18400629D_T4_I2_G1_L1Single-Impact F 24 hour
SA18400717B_T2_I2_G1_L1Single-Impact F 30 min
SA18400815B_T2_I2_G1_L1Single-Impact F 30 min
SA18400929B_T2_I2_G1_L1Single-Impact F 30 min
SA18401027B_T2_I2_G1_L1Single-Impact F 30 min
SA18401113B_T2_I2_G1_L2Single-Impact F 30 min
SA18401227C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401329C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401417C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401515C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401622C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401713C_T3_I2_G1_L1Single-Impact F 4 hour
SA18401813A_T1_I2_G1_L1Single-Impact F Baseline
SA18401929A_T1_I2_G1_L1Single-Impact F Baseline
SA18402015A_T1_I2_G1_L1Single-Impact F Baseline
SA18402127A_T1_I2_G1_L1Single-Impact F Baseline
SA18402222A_T1_I2_G1_L1Single-Impact F Baseline
SA18402317A_T1_I2_G1_L1Single-Impact F Baseline
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Collection:

Collection ID:CO002021
Collection Summary:Approximately 200 µL of whole blood was collected from a tail vein punctured by 20-gauge Precision Glide needles and stored on ice. Whole blood samples were allowed to coagulate at room temperature for 45 minutes. 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.
Collection Protocol ID:A100188
Collection Protocol Comments:All procedures involving Sprague-Dawley rat models were performed in accordance with guidelines set forth in the Guide for the Care and Use of Laboratory Animals (U.S. Department of Health and Human Services, Pub no. 85-23, 1985) and were approved by the Georgia Institute of Technology Institutional Animal Care and Use Committee
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002040
Treatment Summary:A CCI device (Pittsburgh Precision Instruments, Pittsburgh, PA) was used to induce single and repetitive closed-head injuries to the cortex. Prior to injuries, all rat groups were anesthetized with isoflurane (induction: 5% isoflurane; maintenance: 2-3% isoflurane) and a toe pinch was administered to evaluate loss of consciousness and ensure minimal pain during injury. A pneumatic piston on the CCI device with a 5 mm tip diameter was positioned 15 degrees below the vertical axis of the coronal plane to induce injury to the closed skull, 30 s after removal of the isoflurane supply. All injury groups received impacts from the pneumatic piston at a velocity of 5 m/s. The single impact injury group received one injury with a 5 mm head displacement. The repeat injury group received a total of 3 injuries at 2 min intervals, with head displacements of 5 mm, 2 mm, and 2 mm, respectively. Sham-operated animals received a treatment identical to injured animals but excluding the injury procedure. Following final injury, time-to-right was recorded, and animals were monitored to survey the presence of neurological deficits. Animals were returned to home cages and singly housed with soft bedding during recovery.

Sample Preparation:

Sampleprep ID:SP002034
Sampleprep Summary:A standard spiked IPA solution was prepared with 250 µL of SPLASH II Lipidomix and 14.750 mL of IPA. Serum samples were thawed on ice for one hour prior to the addition of the IPA solution in a 1:3 v/v ratio to separate lipids and small non-polar metabolites from proteins. Mixtures of serum and IPA solution were vortexed for 10 s and centrifuged at 16000g for 7 min. The supernatant was then collected for LC-MS analysis. Sample blanks were prepared with 50 µL of LC-MS grade water, and pooled QC samples were prepared from 5 µL aliquots of all study subject serum samples. Serum reference samples from uninjured Sprague-Dawley rat serum were processed in the same manner as study subject serum samples.

Combined analysis:

Analysis ID AN003174 AN003175
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Accucore C30 (50 x 2.1mm,2.1um) Thermo Accucore C30 (50 x 2.1mm,2.1um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo ID-X Orbitrap Tribrid Thermo ID-X Orbitrap Tribrid
Ion Mode POSITIVE NEGATIVE
Units Normalized Peak Area Normalized Peak Area

Chromatography:

Chromatography ID:CH002347
Chromatography Summary:All samples were run in a randomized order over two and a half days of consecutive instrument time. QC samples were interleaved every 24 runs to evaluate LC-MS system stability and to account for time-dependent batch effects.
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C30 (50 x 2.1mm,2.1um)
Column Temperature:60 ℃
Flow Gradient:(Time: A/B) 0 min 80/20, 1 min 40/60, 5 min 30/70, 5.5 min 15/85, 8 min 10/90, 8.2 min 0/100, 10.7 min 80/20, 12 min 80/20
Flow Rate:0.3 mL/min
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS002952
Analysis ID:AN003174
Instrument Name:Thermo ID-X Orbitrap Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS experiments were preformed over a scan range of 150-2000 m/z, maximum ion injection time was set to 200 ms, and orbitrap resolution was 24000. Raw spectral data from LC-MS experiments were pre-processed using Compound Discoverer v3.0.0 software (Thermo Fischer Scientific, Inc., Waltham, MA) and the XCMS web-based application (xcmsonline.scripps.edu). Initial steps involved retention time alignment between samples, peak area integration, peak picking, and QC area normalization. Features eluting with the solvent front or having retention times below 0.75 min were removed to account for potential ion suppression effects in that retention time region. ChemSpider and in-house mzVault database searches were used to obtain a list of tentative IDs based on accurate mass, isotope pattern, and MS/MS data whenever possible. Each lipid feature was identified according to the following confidence levels: (1) compounds matched to existing in house database standards by accurate mass (<2 ppm), isotopic abundance, fragmentation spectrum, and retention time; (2) compounds annotated according to accurate mass, isotopic abundance, and fragmentation consistent with Lipid Maps and Human Metabolome Database (HMDB) entries; (3) accurate mass match matched to Lipid Maps and HMDB entries and fragmentation showing a few matching characteristic fragment ions.
Ion Mode:POSITIVE
Ion Source Temperature:275 ℃
Ion Spray Voltage:3500 V
Source Temperature:320 ℃
  
MS ID:MS002953
Analysis ID:AN003175
Instrument Name:Thermo ID-X Orbitrap Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS experiments were preformed over a scan range of 150-2000 m/z, maximum ion injection time was set to 200 ms, and orbitrap resolution was 24000. Raw spectral data from LC-MS experiments were pre-processed using Compound Discoverer v3.0.0 software (Thermo Fischer Scientific, Inc., Waltham, MA) and the XCMS web-based application (xcmsonline.scripps.edu). Initial steps involved retention time alignment between samples, peak area integration, peak picking, and QC area normalization. Features eluting with the solvent front or having retention times below 0.75 min were removed to account for potential ion suppression effects in that retention time region. ChemSpider and in-house mzVault database searches were used to obtain a list of tentative IDs based on accurate mass, isotope pattern, and MS/MS data whenever possible. Each lipid feature was identified according to the following confidence levels: (1) compounds matched to existing in house database standards by accurate mass (<2 ppm), isotopic abundance, fragmentation spectrum, and retention time; (2) compounds annotated according to accurate mass, isotopic abundance, and fragmentation consistent with Lipid Maps and Human Metabolome Database (HMDB) entries; (3) accurate mass match matched to Lipid Maps and HMDB entries and fragmentation showing a few matching characteristic fragment ions.
Ion Mode:NEGATIVE
Ion Source Temperature:275 ℃
Ion Spray Voltage:-2500 V
Source Temperature:320 ℃
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