Lipid Annotation for LC-MS/MS DIA Data


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Documentation for package ‘LipidMS’ version 1.2.0

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adductsTable Adducts table
assignDB load LipidMS default data bases
baconjdb Bile acids conjugates database
badb Bile acids database
carnitinesdb Carnitines database
CEdb CEs 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: peakpicking and deisotoping
dgdb DGs database
fadb FAs database
fahfadb FAHFAs database
findCandidates Search of lipid candidates of a certain class.
getInclusionList Obtain an inclusion list from the annotation results
hfadb HFAs database
idBAneg Bile Acids (BA) annotation for ESI-
idCarpos Carnitine annotation for ESI+
idCEpos Cholesterol Esthers (CE) annotation for ESI+
idCerneg Ceramides (Cer) annotation for ESI-
idCerpos Ceramides (Cer) 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-
idPCpos Phosphocholines (PC) annotation for ESI+
idPEneg Phosphoethanolamines (PE) annotation for ESI-
idPEpos Phosphoethanolamines (PE) annotation for ESI+
idPGneg Phosphoglycerols (PG) annotation for ESI-
idPIneg Phosphoinositols (PI) annotation for ESI-
idPOS Lipids annotation for ESI+
idPSneg Phosphoserines (PS) 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+
lysopadb LPAs database
lysopcdb LPCs database
lysopedb LPEs 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
pedb PEs database
pgdb PGs database
pidb PIs database
psdb PSs database
searchIsotopes Target isotopes search
sepByCE Separate .mzXML files by CE
smdb SMs database
sphdb Sphingoid bases database
sphPdb Sphingoid bases phosphate database
tgdb TGs database