Lipid Annotation for LC-MS/MS DDA or DIA Data
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Documentation for package ‘LipidMS’ version 3.0.4
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A B C D F G H I L M N O P R S T
-- A --
| acylcerdb | AcylCeramides database |
| adductsTable | Adducts table |
| alignmsbatch | Align samples from an msbatch |
| annotatemsbatch | Lipid annotation for an msbatch |
| assignDB | Load LipidMS default data bases |
-- B --
| 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. |
-- C --
| carnitinesdb | Carnitines database |
| CEdb | CEs database |
| cerdb | Ceramides database |
| cerPdb | Ceramides Phosphate 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 |
-- D --
| dataProcessing | Process mzXML files individually: peakpicking and isotope annotation |
| ddaFrags | MS/MS scan extraction of a precursor in DDA |
| dgdb | DGs database |
-- F --
| fadb | FAs database |
| fahfadb | FAHFAs database |
| fillpeaksmsbatch | Fill peaks from a grouped msbatch |
| findCandidates | Search of lipid candidates of a certain class |
-- G --
| getInclusionList | Obtain an inclusion list from the annotation results |
| groupmsbatch | Group features from an msbatch |
-- H --
| hfadb | HFAs database |
-- I --
| idAcylCerneg | Acylceramides (AcylCer) annotation for ESI- |
| idAcylCerpos | Acylceramides (AcylCer) annotation for ESI+ |
| idBAneg | Bile Acids (BA) annotation for ESI- |
| idCarpos | Acylcarnitine annotation for ESI+ |
| idCEpos | Cholesteryl Esters (CE) annotation for ESI+ |
| idCerneg | Ceramides (Cer) annotation for ESI- |
| idCerPneg | Ceramides phosphate (CerP) annotation for ESI- |
| idCerpos | Ceramides (Cer) annotation for ESI+ |
| idCerPpos | Ceramides phosphate (CerP) annotation for ESI+ |
| idCLneg | Cardiolipines (CL) 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+ |
| idSphneg | Sphingoid bases (Sph) annotation for ESI- |
| idSphPneg | Sphingoid bases phosphate (SphP) annotation for ESI- |
| idSphpos | Sphingoid bases (Sph) annotation for ESI- |
| idSphPpos | Sphingoid bases phosphate (SphP) annotation for ESI+ |
| idTGpos | Triacylglycerols (TG) annotation for ESI+ |
-- L --
| LipidMSapp | LipidMS shiny app |
| 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 |
-- M --
| mgdb | MGs database |
-- N --
| nlsphdb | Neutral losses db for sphingoid bases. It is employed by idCerneg function. |
-- O --
| organizeResults | Prepare output for LipidMS annotation functions |
-- P --
| 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 |
| ploteicmsbatch | EIC for all samples in a msbatch |
| plotLipids | Plot informative peaks for lipid annotation |
| plotticmsbatch | TIC for all samples in a msbatch |
| psdb | PSs database |
-- R --
| rtdevplot | Plot retention time deviation |
-- S --
| searchIsotopes | Targeted isotopes search |
| searchIsotopesmsbatch | Targeted isotopes search for msbatch |
| setmsbatch | Create msbatch for batch processing. |
| smdb | SMs database |
| sphdb | Sphingoid bases database |
| sphPdb | Sphingoid bases phosphate database |
-- T --
| tgdb | TGs database |