LipidMS v1.0.0

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Lipid Annotation for LC-MS/MS DIA Data

Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity rules.

Functions in LipidMS

Name Description
MS1_pos Example MS1 data set for id functions in ESI+
MassLysoPI Calculate formula and mass of LPI
MassLysoPC Calculate formula and mass of LysoPC
MassLysoPE Calculate formula and mass of LPE
MassTG Calculate formula and mass of TG
MassLysoPS Calculate formula and mass of LysoPS
MassMG Calculate formula and mass of MG
adductsTable Adducts table
MSMS2_pos Example MS2 data set for id functions in ESI+ (high energy)
cbs Total number of carbons and double bounds
checkIntRules Check intensity rules
MassCL Calculate formula and mass of CL
MassCarnitines Calculate formula and mass of carnitines
MassHFA Calculate formula and mass of hydroxi fatty acids
MassLysoPA Calculate formula and mass of LPA
MassPA Calculate formula and mass of PA
checkIntensityRules Check intensity rules
MassCE Calculate formula and mass of cholesterol esthers
crossTables Cross the original MS1 peaklist with the annotation results
crossAdducts Cross different candidates tables to remove false positives.
cerdb ceramides database
coelutionScore calculate coelution score between two peaks
coelutingFrags Coeluting fragments extraction
combineChains Combine chain fragments that could belong to the same precursor.
MassPC Calculate formula and mass of PC
cldb Cardiolipins database
MassPIP3 Calculate formula and mass of PIP3
MassPIP2 Calculate formula and mass of PIP2
fahfadb FAHFAs database
fadb FAs database
idCerpos Ceramides (Cer) annotation for ESI+
filtermsms Presence or absence of an mz value withing a vector of mz values
CEdb CEs database
idLPEneg Lysophosphoethanolamines (LPE) annotation for ESI-
idBAneg Bile Acids (BA) annotation for ESI-
hfadb HFAs database
idLPEpos Lysophosphoethanolamines (LPE) annotation for ESI+
idPSneg Phosphoserines (PS) annotation for ESI-
MassCer Calculate formula and mass of ceramides
findCandidates Search of lipid candidates of a certain class.
idFAHFAneg FAHFA annotation for ESI-
idSMpos Sphyngomyelines (SM) annotation for ESI+
idFAneg Fatty Acids (FA) annotation for ESI-
idSphPneg Sphingoid bases phosphate (SphP) annotation for ESI-
idTGpos Triacylglycerols (TG) annotation for ESI+
MassCerP Calculate formula and mass of ceramides phosphate
MassPS Calculate formula and mass of PS
idDGpos Diacylglycerols (DG) annotation for ESI+
MassSM Calculate formula and mass of sphingomyelines
idLPSneg Lysophosphoserines (LPS) annotation for ESI-
idSphPpos Sphingoid bases phosphate (SphP) annotation for ESI+
idMGpos Monoacylglycerol (MG) annotation for ESI+
MS1_neg Example MS1 data set for id functions in ESI-
idPCpos Phosphocholines (PC) annotation for ESI+
lysopidb LPIs database
joinfrags Join fragments information when several peaks of the same fragment are coeluting with a unique candidate
lysopsdb LPSs database
chainFrags Search of chain specific fragments
idPEneg Phosphoethanolamines (PE) annotation for ESI-
psdb PSs database
lysopedb LPEs database
MassFAHFA Calculate formula and mass of FAHFA
MassGlcCer Calculate formula and mass of glucoceramides
mzMatch mz match withing a vector of mz values
checkClass Search of class fragments to confirm the lipid class.
MassPE Calculate formula and mass of PE
dbOneChain Creation of a database for Carnitines, CE, FA, HFA, LPL, MG, sphingoid bases and sphingoid bases phosphate.
lysopgdb LPGs database
MassPG Calculate formula and mass of PG
assignDB load LipidMS default data bases
baconjdb Bile acids conjugates database
smdb SMs database
searchIsotopes Target isotopes search
sphPdb Sphingoid bases phosphate database
badb Bile acids database
MSMS1_pos Example MS2 data set for id functions in ESI+ (low energy)
nlsphdb Neutral losses db for sphingoid bases. It is employed by idCerneg function.
dbSphingolipids Creation of a database for Cer, CerP, GlcCer and SM
MSMS2_neg Example MS2 data set for id functions in ESI- (high energy)
carnitinesdb Carnitines database
dbFourChains Creation of a database for C.
dataProcessing Process mzXML files: peakpicking and deisotoping
MassDG Calculate formula and mass of DG
MassFA Calculate formula and mass of fatty acids
MassPI Calculate formula and mass of PI
dgdb DGs database
MassPIP Calculate formula and mass of PIP
diffcb Difference between two carbon:bounds structures
dbThreeChains Creation of a database for TG.
dbTwoChains Creation of a database for FAHFA, DG and PL.
getFormula Get formula and neutral mass for annotated compounds
getInclusionList Obtain an inclusion list from the annotation results
idCarpos Carnitine annotation for ESI+
idLPGneg Lysophosphoglycerols (LPG) annotation for ESI-
idLPIneg Lysophosphoinositols (LPI) annotation for ESI-
idCerneg Ceramides (Cer) annotation for ESI-
idNEG Lipids annotation for ESI-
idPCneg Phosphocholines (PC) annotation for ESI-
lysopadb LPAs database
MassSph Calculate formula and mass of sphingoid bases
lysopcdb LPCs database
MassSphP Calculate formula and mass of sphingoid phosphate bases
confLevels Confidence Annotation Levels
idPIneg Phosphoinositols (PI) annotation for ESI-
idPOS Lipids annotation for ESI+
createLipidDB Customizable lipid DBs creator
pcdb PCs database
makexcmsSet Convert peaklist from envipick to a xcmxSet to remove isotopes
mgdb MGs database
select Check matches between chains composition and precursor structures
pedb PEs database
sphdb Sphingoid bases database
sepByCE Separate .mzXML files by CE
findPrecursor Find candidate precursor from fullMS function
tgdb TGs database
frags Search for fragments of interest withing a list of coeluting fragments
sumChains Calculate total number of carbons and double bounds of lipid chains
idCEpos Cholesterol Esthers (CE) annotation for ESI+
idCLneg Cardiolipines (CL) annotation for ESI-
idLPCneg Lysophosphocholines (LPC) annotation for ESI-
idLPCpos Lysophosphocholines (LPC) annotation for ESI+
idPEpos Phosphoethanolamines (PE) annotation for ESI+
idPGneg Phosphoglycerols (PG) annotation for ESI-
idSphneg Sphingoid bases (Sph) annotation for ESI-
idSphpos Sphingoid bases (Sph) annotation for ESI-
organizeResults Prepare output for LipidMS annotation functions
padb PAs database
pgdb PGs database
pidb PIs database
MSMS1_neg Example MS2 data set for id functions in ESI- (low energy)
MassLysoPG Calculate formula and mass of LPG
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Vignettes of LipidMS

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abstract.png
vignette.Rmd
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Details

Type Package
License GPL (>= 2)
LazyData TRUE
RoxygenNote 6.1.0
VignetteBuilder knitr
Encoding UTF-8
NeedsCompilation no
Packaged 2018-10-05 11:11:58 UTC; 73581298C
Repository CRAN
Date/Publication 2018-10-15 18:30:03 UTC

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