LipidMS v0.1.0

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Lipid Annotation for LC-MS/MS using Data Independent Acquisition

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

Functions in LipidMS

Name Description
MassGlcCer Calculate formula and mass of glucoceramides
MassPI Calculate formula and mass of PI
idCLneg Cardiolipines (CL) annotation for ESI-
idCarpos Carnitine annotation for ESI+
idPCneg Phosphocholines (PC) annotation for ESI-
idLPEneg Lysophosphoethanolamines (LPE) annotation for ESI-
idLPCpos Lysophosphocholines (LPC) annotation for ESI+
idTGpos Triacylglycerols (TG) annotation for ESI+
MassHFA Calculate formula and mass of hydroxi fatty acids
idSphpos Sphingoid bases (Sph) annotation for ESI-
organizeResults Prepare output for LipidMS annotation functions
idPCpos Phosphocholines (PC) annotation for ESI+
mix_pos_Ce20 Peak list example of MSMS1 obtained from a mix of standards.
mix_neg_fullMS Peak list example of MS1 obtained from a mix of standards.
padb PAs database
sumChains Calculate total number of carbons and double bounds of lipid chains
CEdb CEs database
MassLysoPS Calculate formula and mass of LysoPS
MassSph Calculate formula and mass of sphingoid bases
MassMG Calculate formula and mass of MG
MassCE Calculate formula and mass of cholesterol esthers
baconjdb Bile acids conjugates database
tgdb TGs database
checkClass Search of class fragments to confirm the lipid class.
MassLysoPG Calculate formula and mass of LPG
MassFAHFA Calculate formula and mass of FAHFA
createLipidDB Customizable lipid DBs creator
confLevels Confidence Annotation Levels
MassSM Calculate formula and mass of sphingomyelines
diffcb Difference between two carbon:bounds structures
dbTwoChains Creation of a database for FAHFA, DG and PL.
checkIntRules Check intensity rules
dbOneChain Creation of a database for Carnitines, CE, FA, HFA, LPL, MG, sphingoid bases and sphingoid bases phosphate.
dbFourChains Creation of a database for C.
MassSphP Calculate formula and mass of sphingoid phosphate bases
badb Bile acids database
MassLysoPI Calculate formula and mass of LPI
dgdb DGs database
MassLysoPA Calculate formula and mass of LPA
frags Search for fragments of interest withing a list of coeluting fragments
getFormula Get formula and neutral mass for annotated compounds
MassTG Calculate formula and mass of TG
idFAneg Fatty Acids (FA) annotation for ESI-
fadb FAs database
idCerneg Ceramides (Cer) annotation for ESI-
adductsTable Adducts table
checkIntensityRules Check intensity rules
idLPEpos Lysophosphoethanolamines (LPE) annotation for ESI+
idCerpos Ceramides (Cer) annotation for ESI+
MassPE Calculate formula and mass of PE
MassPG Calculate formula and mass of PG
cldb Cardiolipins database
crossTables Cross the original MS1 peaklist with the annotation results
idLPCneg Lysophosphocholines (LPC) annotation for ESI-
idLPGneg Lysophosphoglycerols (LPG) annotation for ESI-
idSMpos Sphyngomyelines (SM) annotation for ESI+
idSphPneg Sphingoid bases phosphate (SphP) annotation for ESI-
coelutingFrags Coeluting fragments extraction
cbs Total number of carbons and double bounds
dataProcessing Process mzXML files: peakpicking and deisotoping
dbThreeChains Creation of a database for TG.
idBAneg Bile Acids (BA) annotation for ESI-
dbSphingolipids Creation of a database for Cer, CerP, GlcCer and SM
combineChains Combine chain fragments that could belong to the same precursor.
findCandidates Search of lipid candidates of a certain class.
findPrecursor Find candidate precursor from fullMS function
idPGneg Phosphoglycerols (PG) annotation for ESI-
lysopedb LPEs database
getInclusionList Obtain an inclusion list from the annotation results
hfadb HFAs database
idPIneg Phosphoinositols (PI) annotation for ESI-
serum_neg_Ce40 Peak list example of MSMS2 obtained from a pool of serum samples.
lysopgdb LPGs database
serum_neg_fullMS Peak list example of MS1 obtained from a pool of serum samples.
idDGpos Diacylglycerols (DG) annotation for ESI+
sphPdb Sphingoid bases phosphate database
lysopadb LPAs database
idCEpos Cholesterol Esthers (CE) annotation for ESI+
fahfadb FAHFAs database
idFAHFAneg FAHFA annotation for ESI-
idPOS Lipids annotation for ESI+
lysopcdb LPCs database
sphdb Sphingoid bases database
idPSneg Phosphoserines (PS) annotation for ESI-
idLPIneg Lysophosphoinositols (LPI) annotation for ESI-
joinAdducts Join information about precursor candidates found using different adducts
idLPSneg Lysophosphoserines (LPS) annotation for ESI-
idMGpos Monoacylglycerol (MG) annotation for ESI+
idNEG Lipids annotation for ESI-
joinfrags Join fragments information when several peaks of the same fragment are coeluting with a unique candidate
idPEneg Phosphoethanolamines (PE) annotation for ESI-
filtermsms Presence or absence of an mz value withing a vector of mz values
pedb PEs database
pcdb PCs database
makexcmsSet Convert peaklist from envipick to a xcmxSet to remove isotopes
lysopidb LPIs database
mgdb MGs database
sepByCE Separate .mzXML files by CE
idPEpos Phosphoethanolamines (PE) annotation for ESI+
lysopsdb LPSs database
pgdb PGs database
mzMatch mz match withing a vector of mz values
serum_neg_Ce20 Peak list example of MSMS1 obtained from a pool of serum samples.
serum_pos_fullMS Peak list example of MS1 obtained from a pool of serum samples.
pidb PIs database
smdb SMs database
nlsphdb Neutral losses db for sphingoid bases. It is employed by idCerneg function.
serum_pos_Ce20 Peak list example of MSMS1 obtained from a pool of serum samples.
removeDGs remove fragments whose relative intensity to the precursor is less than 10 times smaller
select Check matches between chains composition and precursor structures
idSphneg Sphingoid bases (Sph) annotation for ESI-
idSphPpos Sphingoid bases phosphate (SphP) annotation for ESI+
mix_neg_Ce20 Peak list example of MSMS1 obtained from a mix of standards.
serum_pos_Ce40 Peak list example of MSMS2 obtained from a pool of serum samples.
mix_neg_Ce40 Peak list example of MSMS2 obtained from a mix of standards.
mix_pos_Ce40 Peak list example of MSMS2 obtained from a mix of standards.
psdb PSs database
mix_pos_fullMS Peak list example of MS1 obtained from a mix of standards.
removeAdducts remove wrong assigned adducts
MassCerP Calculate formula and mass of ceramides phosphate
MassCL Calculate formula and mass of CL
MassCer Calculate formula and mass of ceramides
MassPA Calculate formula and mass of PA
MassPC Calculate formula and mass of PC
cerdb ceramides database
chainFrags Search of chain specific fragments
MassCarnitines Calculate formula and mass of carnitines
MassDG Calculate formula and mass of DG
MassFA Calculate formula and mass of fatty acids
MassPIP2 Calculate formula and mass of PIP2
carnitinesdb Carnitines database
MassPIP3 Calculate formula and mass of PIP3
MassLysoPE Calculate formula and mass of LPE
MassLysoPC Calculate formula and mass of LysoPC
MassPS Calculate formula and mass of PS
MassPIP Calculate formula and mass of PIP
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Details

Type Package
License GPL (>= 2)
LazyData TRUE
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2018-07-10 11:59:40 UTC; 73581298C
Repository CRAN
Date/Publication 2018-07-12 10:40:03 UTC

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