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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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Version

Install

install.packages('LipidMS')

Monthly Downloads

327

Version

0.1.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

July 12th, 2018

Functions in LipidMS (0.1.0)

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