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.
| Study ID | ST000920 |
| Study Title | Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics |
| Study Type | Untargeted lipidomics |
| Study 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 | 311 Ferst Dr |
| srjhogan@gatech.edu | |
| Phone | 2156924657 |
| Submit Date | 2018-01-19 |
| Num Groups | 5 |
| Total Subjects | 34 |
| Num Males | 34 |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-04-10 |
| Release Version | 1 |
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 |
| Species Group: | Mammals |
Factors:
Subject type: Rat; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Class |
|---|---|---|
| SA054636 | NA5 | naïve |
| SA054637 | NA1 | naïve |
| SA054638 | NA7 | naïve |
| SA054639 | NA8 | naïve |
| SA054640 | NA2 | naïve |
| SA054641 | NA6 | naïve |
| SA054642 | NA4 | naïve |
| SA054643 | NA3 | naïve |
| SA054644 | NA0 | naïve |
| SA054645 | NA9 | naïve |
| SA054612 | SA7 | SHAM |
| SA054613 | SA3 | SHAM |
| SA054614 | SC7 | SHAM |
| SA054615 | SB3 | SHAM |
| SA054616 | SD7 | SHAM |
| SA054617 | SC3 | SHAM |
| SA054618 | SD3 | SHAM |
| SA054619 | SB7 | SHAM |
| SA054620 | TM3 | TBI |
| SA054621 | TC7 | TBI |
| SA054622 | TP3 | TBI |
| SA054623 | TJ3 | TBI |
| SA054624 | TK3 | TBI |
| SA054625 | TE7 | TBI |
| SA054626 | TI7 | TBI |
| SA054627 | TN3 | TBI |
| SA054628 | TL3 | TBI |
| SA054629 | TG7 | TBI |
| SA054630 | TF7 | TBI |
| SA054631 | TB7 | TBI |
| SA054632 | TD7 | TBI |
| SA054633 | TA7 | TBI |
| SA054634 | TO3 | TBI |
| SA054635 | TH7 | TBI |
| 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 |
