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 ResearchMeSH KeywordsAlgorithmsChromatography, High Pressure LiquidHumansLipidsSoftwareTandem Mass SpectrometryConceptsInternal 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 health
2017
LipidMatch: 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 ResearchMeSH KeywordsAlgorithmsAutomationChromatography, High Pressure LiquidHumansLipidsMolecular WeightSoftwareTandem Mass SpectrometryConceptsLipid 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 ResearchMeSH KeywordsBiomarkersChromatography, High Pressure LiquidChromatography, LiquidLipidsMetabolomicsSoftwareStatistics as TopicTandem Mass SpectrometryWorkflowConceptsHigh-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 lipidomicsChromatography