2022
TidyMass an object-oriented reproducible analysis framework for LC–MS data
Shen X, Yan H, Wang C, Gao P, Johnson CH, Snyder MP. TidyMass an object-oriented reproducible analysis framework for LC–MS data. Nature Communications 2022, 13: 4365. PMID: 35902589, PMCID: PMC9334349, DOI: 10.1038/s41467-022-32155-w.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, LiquidEcosystemMetabolomicsReproducibility of ResultsSoftwareTandem Mass SpectrometryWorkflowConceptsObject-oriented computational frameworkComputational frameworkExtensible toolMetabolomics data analysisData structureWorkflow needsModular architectureOwn pipelinesData processingMultiple toolsAnalysis frameworkDesign philosophyR packageFrameworkLC-MS dataData analysisToolUsersArchitectureTraceabilityPipelineProcessingPackageGrammar
2014
Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling
Benton HP, Ivanisevic J, Mahieu NG, Kurczy ME, Johnson CH, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi BK, Tautenhahn R, Gieschen A, Fields MW, Patti GJ, Siuzdak G. Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling. Analytical Chemistry 2014, 87: 884-891. PMID: 25496351, PMCID: PMC4303330, DOI: 10.1021/ac5025649.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, LiquidComputational BiologyDatabases, FactualDesulfovibrio vulgarisElectronic Data ProcessingMetabolomicsSoftwareTandem Mass SpectrometryConceptsMass spectrometry data acquisitionSystems biology levelMass spectrometry analysisBioinformatics resourcesGlobal profilingTandem mass spectrometry dataProfiling datasetsMass spectrometry databaseMass spectrometry dataSpectrometry analysisProfilingData acquisitionSpectrometry dataRapid metabolite identificationMetabolomic profilingUntargeted metabolomicsBacterial samplesMetabolomicsSimultaneous data processingIdentificationMetabolite identificationMetabolomics workflowsFliesAutomatic searchAutonomous approach