{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000899","ANALYSIS_ID":"AN001464","VERSION":"1","CREATED_ON":"November 14, 2017, 11:11 am"},

"PROJECT":{"PROJECT_TITLE":"Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling","PROJECT_SUMMARY":"Non-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).","INSTITUTE":"Vanderbilt University Medical Center","LAST_NAME":"Scoville","FIRST_NAME":"Elizabeth","ADDRESS":"1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA","EMAIL":"elizabeth.a.scoville@vanderbilt.edu","PHONE":"615-322-5200"},

"STUDY":{"STUDY_TITLE":"Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling","STUDY_SUMMARY":"Non-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).","INSTITUTE":"Vanderbilt University Medical Center","LAST_NAME":"Elizabeth","FIRST_NAME":"Scoville","ADDRESS":"1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA","EMAIL":"elizabeth.a.scoville@vanderbilt.edu","PHONE":"615-322-5200"},

"SUBJECT":{"SUBJECT_TYPE":"Human serum","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"4",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"22",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"25",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"27",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"43",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"49",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"50",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"51",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"52",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"54",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"59",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"67",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"69",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"73",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"75",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"76",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"79",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"86",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"121",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"144",
"Factors":{"Type":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"12",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"18",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"35",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"48",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"56",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"63",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"68",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"71",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"77",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"80",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"88",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"90",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"91",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"125",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"130",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"143",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"157",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"168",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"194",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"197",
"Factors":{"Type":"Ulcerative Colitis"}
},
{
"Subject ID":"-",
"Sample ID":"303",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"304",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"305",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"306",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"309",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"310",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"313",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"318",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"321",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"324",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"327",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"329",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"330",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"333",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"335",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"337",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"341",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"342",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"345",
"Factors":{"Type":"Crohn disease"}
},
{
"Subject ID":"-",
"Sample ID":"347",
"Factors":{"Type":"Crohn disease"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Patients with confirmed UC (n = 20) were recruited from either the outpatient endoscopy unit or IBD clinic at Vanderbilt University Medical Center. Patients with confirmed CD (n = 20) were recruited from the IBD clinic at Vanderbilt University Medical Center. IBD diagnosis was determined by accepted clinical and histologic criteria by an IBD specialist. Non-IBD control subjects (n = 20) were recruited from patients undergoing colonoscopy for colorectal cancer screening or other non-IBD related indications. Individuals who were pregnant, had known coagulopathy or bleeding disorders, known renal or hepatic impairment, prior organ transplant, or were unable to give informed consent were excluded. Blood was collected in a vacutainer without additives and allowed to clot. The sample was centrifuged within an hour of collection and serum was aliquoted. Serum samples were snap frozen with dry ice and then stored at –80°C."},

"TREATMENT":{"TREATMENT_SUMMARY":"Individuals were categorized as either having Crohn disease, Ulcerative colitis, or as non-IBD controls by accepted clinical and histologic criteria by an IBD specialist."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":": All samples were maintained at -80oC until processed. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.","SAMPLEPREP_PROTOCOL_FILENAME":"SupplementalMaterial1.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient-eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). A 2nd aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA and was operated at an overall higher organic content. A 3rd aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM ammonium bicarbonate at pH 8.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2.1mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Waters ACQUITY ultra-performance liquid chromatography (UPLC) Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution","RESOLUTION_SETTING":"35,000"},

"MS_METABOLITE_DATA":{
"Units":"raw area counts",

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}