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LipidMS (version 0.1.0)
Lipid Annotation for LC-MS/MS using Data Independent Acquisition
Description
Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation rules.
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Install
install.packages('LipidMS')
Monthly Downloads
432
Version
0.1.0
License
GPL (>= 2)
Maintainer
M Alcoriza-Balaguer
Last Published
July 12th, 2018
Functions in LipidMS (0.1.0)
Search functions
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