Assessment of Metabolome Annotation Quality A Method for Evaluating the False Discovery Rate of Elemental Composition Searches 英文参考文献.docVIP

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Assessment of Metabolome Annotation Quality A Method for Evaluating the False Discovery Rate of Elemental Composition Searches 英文参考文献.doc

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Assessment of Metabolome Annotation Quality A Method for Evaluating the False Discovery Rate of Elemental Composition Searches 英文参考文献

AssessmentofMetabolomeAnnotationQuality:A MethodforEvaluatingtheFalseDiscoveryRateof ElementalCompositionSearches FumioMatsuda1,YokoShinbo2,AkiraOikawa1,MasamiYokotaHirai1,3,OliverFiehn4 ,Shigehiko Kanaya1,2,3,KazukiSaito1,5 * 1Metabolome Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan, 2Graduate School of Information Science, Nara Institute of Science and Technology,Ikoma,Nara,Japan,3JapanScienceandTechnologyAgency,CREST,Kawaguchi,Saitama,Japan,4MetabolomicsResearchLaboratory,UCDavisGenome Center,Davis,California,UnitedStatesofAmerica,5GraduateSchoolofPharmaceuticalSciences,ChibaUniversity,Chiba,Japan Abstract Background:Inmetabolomicsresearchesusingmassspectrometry(MS),systematicsearchingofhigh-resolutionmassdata against compound databases is often the first step of metabolite annotation to determine elemental compositions possessingsimilartheoreticalmassnumbers.However,incorrecthitsderivedfromerrorsinmassanalyseswillbeincludedin theresultsofelementalcompositionsearches.Toassessthequalityofpeakannotationinformation,anovelmethodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databasesmostreliableforsearchingarediscussed. Methodology/PrincipalFindings:TheFDRcanbedeterminedfromonemeasuredvalue(i.e.,thehitrateforsearchqueries) andfourparametersdeterminedbyMonteCarlosimulation.TheresultsindicatethatrelativelyhighFDRvalues(30–50%) wereobtainedwhensearchingtime-of-flight(TOF)/MSdatausingtheKNApSAcKandKEGGdatabases.Inaddition,searches againstlargeall-in-onedatabases(e.g.,PubChem)alwaysproducedunacceptableresults(FDR.70%).TheestimatedFDRs suggestthatthequalityofsearchresultscanbeimprovednotonlybyperformingmoreaccuratemassanalysisbutalsoby modifyingthepropertiesofthecompounddatabase.AtheoreticalanalysisindicatesthatFDRcouldbeimprovedbyusing compounddatabasewit