CEdb                    CEs database
LipidMSapp              LipidMS shiny app
acylcerdb               AcylCeramides database
adductsTable            Adducts table
alignmsbatch            Align samples from an msbatch
annotatemsbatch         Lipid annotation for an msbatch
assignDB                Load LipidMS default data bases
baconjdb                Bile acids conjugates database
badb                    Bile acids database
batchdataProcessing     Process several mzXML files (peakpicking and
                        isotope annotation) and create an msbatch for
                        batch processing.
carnitinedb             Carnitine database
cerPdb                  Ceramides Phosphate database
cerdb                   Ceramides database
chainFrags              Search of chain specific fragments
checkClass              Search of class fragments to confirm the lipid
                        class.
checkIntensityRules     Check intensity rules
cldb                    Cardiolipins database
coelutingFrags          Coeluting fragments extraction
coelutionScore          calculate coelution score between two peaks
combineChains           Combine chain fragments that could belong to
                        the same precursor.
confLevels              Confidence Annotation Levels
createLipidDB           Customizable lipid DBs creator
crossTables             Cross the original MS1 peaklist with the
                        annotation results
dataProcessing          Process mzXML files individually: peakpicking
                        and isotope annotation
ddaFrags                MS/MS scan extraction of a precursor in DDA
dgdb                    DGs database
fadb                    FAs database
fahfadb                 FAHFAs database
fillpeaksmsbatch        Fill peaks from a grouped msbatch
findCandidates          Search of lipid candidates of a certain class
getInclusionList        Obtain an inclusion list from the annotation
                        results
groupmsbatch            Group features from an msbatch
hfadb                   HFAs database
idAcylCerneg            Acylceramides (AcylCer) annotation for ESI-
idAcylCerpos            Acylceramides (AcylCer) annotation for ESI+
idBAneg                 Bile Acids (BA) annotation for ESI-
idCEpos                 Cholesteryl Esters (CE) annotation for ESI+
idCLneg                 Cardiolipines (CL) annotation for ESI-
idCarpos                Acylcarnitine annotation for ESI+
idCerPneg               Ceramides phosphate (CerP) annotation for ESI-
idCerPpos               Ceramides phosphate (CerP) annotation for ESI+
idCerneg                Ceramides (Cer) annotation for ESI-
idCerpos                Ceramides (Cer) annotation for ESI+
idDGpos                 Diacylglycerols (DG) annotation for ESI+
idFAHFAneg              FAHFA annotation for ESI-
idFAneg                 Fatty Acids (FA) annotation for ESI-
idLPCneg                Lysophosphocholines (LPC) annotation for ESI-
idLPCpos                Lysophosphocholines (LPC) annotation for ESI+
idLPEneg                Lysophosphoethanolamines (LPE) annotation for
                        ESI-
idLPEpos                Lysophosphoethanolamines (LPE) annotation for
                        ESI+
idLPGneg                Lysophosphoglycerols (LPG) annotation for ESI-
idLPIneg                Lysophosphoinositols (LPI) annotation for ESI-
idLPSneg                Lysophosphoserines (LPS) annotation for ESI-
idMGpos                 Monoacylglycerol (MG) annotation for ESI+
idNEG                   Lipids annotation for ESI-
idPCneg                 Phosphocholines (PC) annotation for ESI-
idPConeg                Plasmanyl Phosphocholines (PCo) annotation for
                        ESI-
idPCopos                Plasmanyl Phosphocholines (PCo) annotation for
                        ESI+
idPCpneg                Plasmenyl Phosphocholines (PCp) annotation for
                        ESI-
idPCpos                 Phosphocholines (PC) annotation for ESI+
idPCppos                Plasmenyl Phosphocholines (PCp) annotation for
                        ESI+
idPEneg                 Phosphoethanolamines (PE) annotation for ESI-
idPEoneg                Plasmanyl Phosphoethanolamines (PEo) annotation
                        for ESI-
idPEopos                Plasmanyl Phosphoethanolamines (PEo) annotation
                        for ESI+
idPEpneg                Plasmenyl Phosphoethanolamines (PEp) annotation
                        for ESI-
idPEpos                 Phosphoethanolamines (PE) annotation for ESI+
idPEppos                Plasmenyl Phosphoethanolamines (PEp) annotation
                        for ESI+
idPGneg                 Phosphoglycerols (PG) annotation for ESI-
idPGpos                 Phosphoglycerols (PG) annotation for ESI+
idPIneg                 Phosphoinositols (PI) annotation for ESI-
idPIpos                 Phosphoinositols (PI) annotation for ESI+
idPOS                   Lipids annotation for ESI+
idPSneg                 Phosphoserines (PS) annotation for ESI-
idSMneg                 Sphingomyelines (SM) annotation for ESI-
idSMpos                 Sphyngomyelines (SM) annotation for ESI+
idSphPneg               Sphingoid bases phosphate (SphP) annotation for
                        ESI-
idSphPpos               Sphingoid bases phosphate (SphP) annotation for
                        ESI+
idSphneg                Sphingoid bases (Sph) annotation for ESI-
idSphpos                Sphingoid bases (Sph) annotation for ESI-
idTGpos                 Triacylglycerols (TG) annotation for ESI+
lysopadb                LPAs database
lysopaodb               O-LPA database
lysopcdb                LPCs database
lysopcodb               O-LPC database
lysopcpdb               P-LPC database
lysopedb                LPEs database
lysopeodb               O-LPE database
lysopepdb               P-LPE database
lysopgdb                LPGs database
lysopidb                LPIs database
lysopsdb                LPSs database
mgdb                    MGs database
nlsphdb                 Neutral losses db for sphingoid bases. It is
                        employed by idCerneg function.
organizeResults         Prepare output for LipidMS annotation functions
padb                    PAs database
pcdb                    PCs database
pcodb                   O-PC database
pcpdb                   P-PC database
pedb                    PEs database
peodb                   O-PE database
pepdb                   P-PE database
pgdb                    PGs database
pidb                    PIs database
plotLipids              Plot informative peaks for lipid annotation
ploteicmsbatch          EIC for all samples in a msbatch
plotticmsbatch          TIC for all samples in a msbatch
psdb                    PSs database
rtdevplot               Plot retention time deviation
searchIsotopes          Targeted isotopes search
searchIsotopesmsbatch   Targeted isotopes search for msbatch
setmsbatch              Create msbatch for batch processing.
smdb                    SMs database
sphPdb                  Sphingoid bases phosphate database
sphdb                   Sphingoid bases database
tgdb                    TGs database
