# Lipid Annotation for LC-MS/MS DDA or DIA Data

## Documentation for package ‘LipidMS’ version 3.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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