2019
Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values
Koelmel J, Cochran J, Ulmer C, Levy A, Patterson R, Olsen B, Yost R, Bowden J, Garrett T. Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values. BMC Bioinformatics 2019, 20: 217. PMID: 31035918, PMCID: PMC6489209, DOI: 10.1186/s12859-019-2803-8.Peer-Reviewed Original ResearchConceptsInternal standardClose retention timesLC-MS/MS studiesMultiple internal standardsTarget analytesLipidomics workflowsLipid standardsMS studiesNormalization of lipidsPeak areaAdductsLipid structureFeature findingAnalytesHuman plasmaBiological systemsLipid classesIndividual internal standardsEther-linked phosphatidylcholinesClinical utilityRetention timeClinical diagnosisQuantitation processLipid speciesUnderstanding of healthLipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa
Koelmel J, Ulmer C, Fogelson S, Jones C, Botha H, Bangma J, Guillette T, Luus-Powell W, Sara J, Smit W, Albert K, Miller H, Guillette M, Olsen B, Cochran J, Garrett T, Yost R, Bowden J. Lipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa. Metabolomics 2019, 15: 38. PMID: 30838461, PMCID: PMC11005104, DOI: 10.1007/s11306-019-1490-9.Peer-Reviewed Original ResearchConceptsApplication of lipidomicsDiverse biological rolesWildlife studiesPossible disease mechanismsClasses of lipidsHigh-resolution tandem mass spectrometryLoskop DamBiological roleMozambique tilapiaCell deathMortality eventsPansteatitisLipidomicsOxidative damageDisease mechanismsAdipose tissuePromising biomarker candidatesBiomarker discoveryDisease etiologyTilapiaTandem mass spectrometryCeramideAquatic lifeLipidomeBiomarker candidates
2018
NIST lipidomics workflow questionnaire: an assessment of community-wide methodologies and perspectives
Bowden J, Ulmer C, Jones C, Koelmel J, Yost R. NIST lipidomics workflow questionnaire: an assessment of community-wide methodologies and perspectives. Metabolomics 2018, 14: 53. PMID: 30830346, PMCID: PMC11493135, DOI: 10.1007/s11306-018-1340-1.Peer-Reviewed Original Research
2017
LipidQC: Method Validation Tool for Visual Comparison to SRM 1950 Using NIST Interlaboratory Comparison Exercise Lipid Consensus Mean Estimate Values
Ulmer C, Ragland J, Koelmel J, Heckert A, Jones C, Garrett T, Yost R, Bowden J. LipidQC: Method Validation Tool for Visual Comparison to SRM 1950 Using NIST Interlaboratory Comparison Exercise Lipid Consensus Mean Estimate Values. Analytical Chemistry 2017, 89: 13069-13073. PMID: 29148710, PMCID: PMC11493136, DOI: 10.1021/acs.analchem.7b04042.Peer-Reviewed Original ResearchLipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data
Koelmel J, Kroeger N, Ulmer C, Bowden J, Patterson R, Cochran J, Beecher C, Garrett T, Yost R. LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. BMC Bioinformatics 2017, 18: 331. PMID: 28693421, PMCID: PMC5504796, DOI: 10.1186/s12859-017-1744-3.Peer-Reviewed Original ResearchConceptsLipid identificationNumerous biological functionsHigh-resolution tandem mass spectrometry dataMass spectrometry workflowsUncharacterized adductsBiological functionsLipid typeStructural detailsLipid-based biomarkersPathway perturbationsTandem mass spectrometry dataSpectral similarity scoreCorrect annotationLipid speciesMass spectrometry dataLiquid chromatography-tandem mass spectrometry (LC-MS/MS) workflowSilico FragmentMass spectrometry experimentsLipid candidatesEtiology of diseaseLipid moleculesAnnotationFatty acyl constituentsBiomarker discoveryDisease etiologyA Robust Lipidomics Workflow for Mammalian Cells, Plasma, and Tissue Using Liquid-Chromatography High-Resolution Tandem Mass Spectrometry
Ulmer C, Patterson R, Koelmel J, Garrett T, Yost R. A Robust Lipidomics Workflow for Mammalian Cells, Plasma, and Tissue Using Liquid-Chromatography High-Resolution Tandem Mass Spectrometry. Methods In Molecular Biology 2017, 1609: 91-106. PMID: 28660577, PMCID: PMC6170197, DOI: 10.1007/978-1-4939-6996-8_10.Peer-Reviewed Original ResearchConceptsHigh-resolution mass spectrometryLipid coverageMass spectrometryResolution tandem mass spectrometryLiquid chromatographyTandem mass spectrometric approachMass spectrometric approachTandem mass spectrometryIdentification of lipidsHigh sample throughputLipidomics workflowsPerformance liquid chromatographyNatural productsSpectrometric approachFatty acid acyl chainsSample preparationStructural diversityDrug discoverySample throughputAcyl chainsSpectrometryLipidomicsSample typesUntargeted lipidomicsChromatographyCommon cases of improper lipid annotation using high-resolution tandem mass spectrometry data and corresponding limitations in biological interpretation
Koelmel J, Ulmer C, Jones C, Yost R, Bowden J. Common cases of improper lipid annotation using high-resolution tandem mass spectrometry data and corresponding limitations in biological interpretation. Biochimica Et Biophysica Acta (BBA) - Molecular And Cell Biology Of Lipids 2017, 1862: 766-770. PMID: 28263877, PMCID: PMC5584053, DOI: 10.1016/j.bbalip.2017.02.016.Peer-Reviewed Original ResearchLipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics
Ulmer C, Koelmel J, Ragland J, Garrett T, Bowden J. LipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics. Journal Of The American Society For Mass Spectrometry 2017, 28: 562-565. PMID: 28074328, PMCID: PMC5557379, DOI: 10.1007/s13361-016-1579-6.Peer-Reviewed Original ResearchConceptsLipid speciesMass spectrometric techniquesNumber of carbonsUnique lipid speciesMass spectrometric analysisLipid oxidation productsMolecular formulaExact massCompound DiscovererChromatographic separationOxidation productsSpectrometric techniquesSample matrixLipid class levelsZ valuesAdduct massesLipid librarySpectrometric analysisDegree of unsaturationInclusion listIsotopic patternsEther-linked lipidsFragmentation experimentsBiological systemsFatty acyl constituents