Man pages for LipidMS
Lipid Annotation for LC-MS/MS DDA or DIA Data

adductsTableAdducts table
annotateIsotopesAnnotate isotopes
assignDBLoad LipidMS default data bases
baconjdbBile acids conjugates database
badbBile acids database
carnitinesdbCarnitines database
cbsTotal number of carbons and double bounds
CEdbCEs database
cerdbCeramides database
chainFragsSearch of chain specific fragments
checkClassSearch of class fragments to confirm the lipid class.
checkIntensityRulesCheck intensity rules
checkIntRulesCheck intensity rules
cldbCardiolipins database
clusteringEIC extraction based on previous partitions generated by...
coelutingFragsCoeluting fragments extraction
coelutionScorecalculate coelution score between two peaks
combineChainsCombine chain fragments that could belong to the same...
confLevelsConfidence Annotation Levels
createLipidDBCustomizable lipid DBs creator
crossAdductsCross different candidates tables to remove false positives.
crossTablesCross the original MS1 peaklist with the annotation results
dataProcessingProcess mzXML files: peakpicking and deisotoping
dbFourChainsCreation of a database for C.
dbOneChainCreation of a database for Carnitines, CE, FA, HFA, LPL, MG,...
dbSphingolipidsCreation of a database for Cer, CerP, GlcCer and SM
dbThreeChainsCreation of a database for TG.
dbTwoChainsCreation of a database for FAHFA, DG and PL.
ddaFragsMS/MS scan extraction of a precursor in DDA
dgdbDGs database
diffcbDifference between two carbon:bounds structures
fadbFAs database
fahfadbFAHFAs database
filtermsmsPresence or absence of an mz value withing a vector of mz...
filtrateAdductsRemove low adduct supported candidates to avoid false...
findCandidatesSearch of lipid candidates of a certain class
findMS2precursorfind lisnks between MS1 peaks and precursors selected for MS2...
findPrecursorFind candidate precursor from fullMS function
fragsSearch for fragments of interest withing a list of coeluting...
getFormulaGet formula and neutral mass for annotated compounds
getInclusionListObtain an inclusion list from the annotation results
hfadbHFAs database
idBAnegBile Acids (BA) annotation for ESI-
idCarposAcylcarnitine annotation for ESI+
idCEposCholesteryl Esters (CE) annotation for ESI+
idCernegCeramides (Cer) annotation for ESI-
idCerposCeramides (Cer) annotation for ESI+
idCLnegCardiolipines (CL) annotation for ESI-
idDGposDiacylglycerols (DG) annotation for ESI+
idFAHFAnegFAHFA annotation for ESI-
idFAnegFatty Acids (FA) annotation for ESI-
idLPCnegLysophosphocholines (LPC) annotation for ESI-
idLPCposLysophosphocholines (LPC) annotation for ESI+
idLPEnegLysophosphoethanolamines (LPE) annotation for ESI-
idLPEposLysophosphoethanolamines (LPE) annotation for ESI+
idLPGnegLysophosphoglycerols (LPG) annotation for ESI-
idLPInegLysophosphoinositols (LPI) annotation for ESI-
idLPSnegLysophosphoserines (LPS) annotation for ESI-
idMGposMonoacylglycerol (MG) annotation for ESI+
idNEGLipids annotation for ESI-
idPCnegPhosphocholines (PC) annotation for ESI-
idPCposPhosphocholines (PC) annotation for ESI+
idPEnegPhosphoethanolamines (PE) annotation for ESI-
idPEposPhosphoethanolamines (PE) annotation for ESI+
idPGnegPhosphoglycerols (PG) annotation for ESI-
idPGposPhosphoglycerols (PG) annotation for ESI+
idPInegPhosphoinositols (PI) annotation for ESI-
idPOSLipids annotation for ESI+
idPSnegPhosphoserines (PS) annotation for ESI-
idSMposSphyngomyelines (SM) annotation for ESI+
idSphnegSphingoid bases (Sph) annotation for ESI-
idSphPnegSphingoid bases phosphate (SphP) annotation for ESI-
idSphposSphingoid bases (Sph) annotation for ESI-
idSphPposSphingoid bases phosphate (SphP) annotation for ESI+
idTGposTriacylglycerols (TG) annotation for ESI+
joinfragsJoin fragments information when several peaks of the same...
LipidMSappLipidMS shiny app
lysopadbLPAs database
lysopcdbLPCs database
lysopedbLPEs database
lysopgdbLPGs database
lysopidbLPIs database
lysopsdbLPSs database
MassCarnitinesCalculate formula and mass of carnitines
MassCECalculate formula and mass of cholesterol esthers
MassCerCalculate formula and mass of ceramides
MassCerPCalculate formula and mass of ceramides phosphate
MassCLCalculate formula and mass of CL
MassDGCalculate formula and mass of DG
MassFACalculate formula and mass of fatty acids
MassFAHFACalculate formula and mass of FAHFA
MassGlcCerCalculate formula and mass of glucoceramides
MassHFACalculate formula and mass of hydroxi fatty acids
MassLysoPACalculate formula and mass of LPA
MassLysoPAoCalculate formula and mass of LPAo
MassLysoPCCalculate formula and mass of LysoPC
MassLysoPCoCalculate formula and mass of LysoPCo
MassLysoPCpCalculate formula and mass of LysoPCp
MassLysoPECalculate formula and mass of LPE
MassLysoPEoCalculate formula and mass of LPEo
MassLysoPEpCalculate formula and mass of LPEp
MassLysoPGCalculate formula and mass of LPG
MassLysoPICalculate formula and mass of LPI
MassLysoPSCalculate formula and mass of LysoPS
MassMGCalculate formula and mass of MG
MassPACalculate formula and mass of PA
MassPCCalculate formula and mass of PC
MassPCoCalculate formula and mass of PCo
MassPCpCalculate formula and mass of PCp
MassPECalculate formula and mass of PE
MassPEoCalculate formula and mass of plasmanyl PE
MassPEpCalculate formula and mass of plasmenyl PE
MassPGCalculate formula and mass of PG
MassPICalculate formula and mass of PI
MassPIPCalculate formula and mass of PIP
MassPIP2Calculate formula and mass of PIP2
MassPIP3Calculate formula and mass of PIP3
MassPSCalculate formula and mass of PS
MassSMCalculate formula and mass of sphingomyelines
MassSphCalculate formula and mass of sphingoid bases
MassSphPCalculate formula and mass of sphingoid phosphate bases
MassTGCalculate formula and mass of TG
mgdbMGs database
mzMatchmz match withing a vector of mz values
nlsphdbNeutral losses db for sphingoid bases. It is employed by...
organizeResultsPrepare output for LipidMS annotation functions
padbPAs database
partitioningagglomarative partitioning for LC-HRMS data based on enviPick...
pcdbPCs database
peakdetectionpeak-pick based on previous EIC clusters generated by...
pedbPEs database
pgdbPGs database
pidbPIs database
plotLipidsPlot informative peaks for lipids annotation
psdbPSs database
readMSfileRead .mzXML files and initiate msobject
searchIsotopesTarget isotopes search
selectCheck matches between chains composition and precursor...
smdbSMs database
sphdbSphingoid bases database
sphPdbSphingoid bases phosphate database
sumChainsCalculate total number of carbons and double bounds of lipid...
tgdbTGs database
LipidMS documentation built on March 18, 2021, 5:08 p.m.