{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000920","ANALYSIS_ID":"AN001508","VERSION":"1","CREATED_ON":"January 19, 2018, 11:56 am"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"srjhogan@gatech.edu","PHONE":"2156924657","NUM_GROUPS":"5","TOTAL_SUBJECTS":"34","NUM_MALES":"34"},

"SUBJECT":{"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"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"TC7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TL3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TN3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TI7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TK3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TE7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TF7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TG7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TH7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TO3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TA7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TB7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TD7",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TJ3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TP3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"TM3",
"Factors":{"Class":"TBI"}
},
{
"Subject ID":"-",
"Sample ID":"SA3",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA8",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"SC7",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"SA7",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA6",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"SB3",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA2",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"NA4",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"SC3",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA3",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"NA0",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"SD7",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA9",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"NA7",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"NA5",
"Factors":{"Class":"naïve"}
},
{
"Subject ID":"-",
"Sample ID":"SD3",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"SB7",
"Factors":{"Class":"SHAM"}
},
{
"Subject ID":"-",
"Sample ID":"NA1",
"Factors":{"Class":"naïve"}
}
],
"COLLECTION":{"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_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"},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity H-Class","COLUMN_NAME":"Acquity BEH C18","FLOW_RATE":".3 mL/min","COLUMN_TEMPERATURE":"60° C","SOLVENT_A":"water: acetonitrile (40:60) + 10 mM ammonium formate + 0.1% formic acid","SOLVENT_B":"10% acetonitrile in IPA + 10 mM ammonium formate + 0.1% formic acid"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","SOFTWARE_VERSION":"MassLyxnx V4.1"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Waters Synapt G2 QTOF","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_RESULTS_FILE":"ST000920_AN001508_Results.txt UNITS:normalized abundance"}

}