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LipidMS v3.1

Lipid Annotation for LC-MS/MS DIA and DDA data analysis.

  • Improved GUI through shiny app running LipidMSapp().

Citation:

If you use this software in your research, please cite:

  • Alcoriza-Balaguer MI., et al. (2019) LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics. Anal Chem, 2019, 91(1), 836-845. doi:10.1021/acs.analchem.8b03409.
  • LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation. Bioinformatics, 2022. doi.org/10.1093/bioinformatics/btac581

References:

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Version

Install

install.packages('LipidMS')

Monthly Downloads

369

Version

3.1.3

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

March 23rd, 2026

Functions in LipidMS (3.1.3)

MassPC

Calculate formula and mass of PC
MassLysoPS

Calculate formula and mass of LysoPS
MassLysoPI

Calculate formula and mass of LPI
MassPCo

Calculate formula and mass of PCo
MassPA

Calculate formula and mass of PA
MassPE

Calculate formula and mass of PE
MassMG

Calculate formula and mass of MG
MassPCp

Calculate formula and mass of PCp
MassPEo

Calculate formula and mass of plasmanyl PE
MassPI

Calculate formula and mass of PI
MassPG

Calculate formula and mass of PG
MassPEp

Calculate formula and mass of plasmenyl PE
annotatemsbatch

Lipid annotation for an msbatch
assignDB

Load LipidMS default data bases
baconjdb

Bile acids conjugates database
MassLysoPG

Calculate formula and mass of LPG
MassLysoPEp

Calculate formula and mass of LPEp
MassPIP3

Calculate formula and mass of PIP3
badb

Bile acids database
MassPS

Calculate formula and mass of PS
MassPIP

Calculate formula and mass of PIP
alignmsbatch

Align samples from an msbatch
acylcerdb

AcylCeramides database
MassSphP

Calculate formula and mass of sphingoid phosphate bases
MassPIP2

Calculate formula and mass of PIP2
annotateIsotopes

Annotate isotopes
MassTG

Calculate formula and mass of TG
MassSph

Calculate formula and mass of sphingoid bases
adductsTable

Adducts table
MassSM

Calculate formula and mass of sphingomyelines
chainFrags

Search of chain specific fragments
checkIntensityRules

Check intensity rules
checkClass

Search of class fragments to confirm the lipid class.
batchdataProcessing

Process several mzXML files (peakpicking and isotope annotation) and create an msbatch for batch processing.
cerdb

Ceramides database
cbs

Total number of carbons and double bounds
chains

extract chains composition from a lipid name
cerPdb

Ceramides Phosphate database
checkIntRules

Check intensity rules
combineChains

Combine chain fragments that could belong to the same precursor.
clustering

EIC extraction based on previous partitions generated by partitioning
clustdist

Calculate max distance between clusters.
combineClassesAdducts

Creates a list that maps lipid classes with their database name and default adducts.
carnitinedb

Carnitine database
clust

Clustering for MS peaks based on mz or RT.
createLipidDB

Customizable lipid DBs creator
cldb

Cardiolipins database
confLevels

Confidence Annotation Levels
coelutingFrags

Coeluting fragments extraction
coelutionScore

calculate coelution score between two peaks
dataProcessing

Process mzXML files individually: peakpicking and isotope annotation
crossTables

Cross the original MS1 peaklist with the annotation results
crossAdducts

Cross different candidates tables to remove false positives.
dbSphingolipids

Creation of a database for Cer, CerP, GlcCer and SM
dbPlasmalogens

Creation of a database for PCo, PCp, PEo and PEp
dbFourChains

Creation of a database for C.
dbTwoChains

Creation of a database for FAHFA, DG and PL.
dbOneChain

Creation of a database for Carnitines, CE, FA, HFA, LPL, MG, sphingoid bases and sphingoid bases phosphate.
dbsAdducts

Create tables containing the m/z of lipids along with their preferred adducts
dbThreeChains

Creation of a database for TG.
filtrateAdducts

Remove low adduct supported candidates to avoid false positives.
findCandidates

Search of lipid candidates of a certain class
ddaFrags

MS/MS scan extraction of a precursor in DDA
fillpeaksmsbatch

Fill peaks from a grouped msbatch
diffcb

Difference between two carbon:bounds structures
fahfadb

FAHFAs database
dgdb

DGs database
.with_future_plan

Temporarily set a future plan and globals max size while running a block
filtermsms

Presence or absence of an mz value within a vector of mz values
idAcylCerneg

Acylceramides (AcylCer) annotation for ESI-
groupmsbatch

Group features from an msbatch
fadb

FAs database
getFormula

Get formula and neutral mass for annotated compounds
frags

Search for fragments of interest withing a list of coeluting fragments
getInclusionList

Obtain an inclusion list from the annotation results
getallpeaks

Extract peaks from all msobjects in a msbatch.
hfadb

HFAs database
findMS2precursor

find lisnks between MS1 peaks and precursors selected for MS2 in DDA
findPrecursor

Find candidate precursor from fullMS function
getfeaturestable

Write features table based on groups
idDGpos

Diacylglycerols (DG) annotation for ESI+
idCLneg

Cardiolipines (CL) annotation for ESI-
idCerPneg

Ceramides phosphate (CerP) annotation for ESI-
idCarpos

Acylcarnitine annotation for ESI+
idCEpos

Cholesteryl Esters (CE) annotation for ESI+
idCerPpos

Ceramides phosphate (CerP) annotation for ESI+
idCerpos

Ceramides (Cer) annotation for ESI+
idBAneg

Bile Acids (BA) annotation for ESI-
idAcylCerpos

Acylceramides (AcylCer) annotation for ESI+
idCerneg

Ceramides (Cer) annotation for ESI-
idLPIneg

Lysophosphoinositols (LPI) annotation for ESI-
idLPEneg

Lysophosphoethanolamines (LPE) annotation for ESI-
idLPEpos

Lysophosphoethanolamines (LPE) annotation for ESI+
idLPCpos

Lysophosphocholines (LPC) annotation for ESI+
idMGpos

Monoacylglycerol (MG) annotation for ESI+
idLPSneg

Lysophosphoserines (LPS) annotation for ESI-
idLPCneg

Lysophosphocholines (LPC) annotation for ESI-
idFAneg

Fatty Acids (FA) annotation for ESI-
idLPGneg

Lysophosphoglycerols (LPG) annotation for ESI-
idFAHFAneg

FAHFA annotation for ESI-
idPConeg

Plasmanyl Phosphocholines (PCo) annotation for ESI-
idPCpos

Phosphocholines (PC) annotation for ESI+
idPCppos

Plasmenyl Phosphocholines (PCp) annotation for ESI+
idNEG

Lipids annotation for ESI-
idPEopos

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+
idPCpneg

Plasmenyl Phosphocholines (PCp) annotation for ESI-
idPEoneg

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-
idPEneg

Phosphoethanolamines (PE) annotation for ESI-
idPCopos

Plasmanyl Phosphocholines (PCo) annotation for ESI+
idPCneg

Phosphocholines (PC) annotation for ESI-
idPEpos

Phosphoethanolamines (PE) annotation for ESI+
idPSneg

Phosphoserines (PS) annotation for ESI-
idPOS

Lipids annotation for ESI+
idPGpos

Phosphoglycerols (PG) annotation for ESI+
idSMneg

Sphingomyelines (SM) annotation for ESI-
idPEppos

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+
idPGneg

Phosphoglycerols (PG) annotation for ESI-
idPEpneg

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-
idPIpos

Phosphoinositols (PI) annotation for ESI+
idPIneg

Phosphoinositols (PI) annotation for ESI-
joinAnnotationResults

Summarize annotation results from an msbatch into the features table
idSphPneg

Sphingoid bases phosphate (SphP) annotation for ESI-
idSphneg

Sphingoid bases (Sph) annotation for ESI-
idSphpos

Sphingoid bases (Sph) annotation for ESI-
idSMpos

Sphyngomyelines (SM) annotation for ESI+
idTGpos

Triacylglycerols (TG) annotation for ESI+
idSphPpos

Sphingoid bases phosphate (SphP) annotation for ESI+
joinfrags

Join fragments information when several peaks of the same fragment are coeluting with a unique candidate
indexrtpart

Index partitions or clusters assigned during alignment.
lysopadb

LPAs database
lysopepdb

P-LPE database
lysopidb

LPIs database
lysopsdb

LPSs database
lysopcpdb

P-LPC database
lysopaodb

O-LPA database
lysopcodb

O-LPC database
lysopcdb

LPCs database
lysopedb

LPEs database
lysopeodb

O-LPE database
partitioning

agglomarative partitioning for LC-HRMS data based on enviPick algorithm
padb

PAs database
mgdb

MGs database
lysopgdb

LPGs database
organizeResults

Prepare output for LipidMS annotation functions
ploteicmsbatch

EIC for all samples in a msbatch
peakdetection

peak-pick based on previous EIC clusters generated by clustering
pepdb

P-PE database
psdb

PSs database
pcpdb

P-PC database
pedb

PEs database
pcodb

O-PC database
nlsphdb

Neutral losses db for sphingoid bases. It is employed by idCerneg function.
mzMatch

mz match withing a vector of mz values
pcdb

PCs database
plotticmsbatch

TIC for all samples in a msbatch
plotLipids

Plot informative peaks for lipid annotation
searchIsotopes

Targeted isotopes search
pgdb

PGs database
pidb

PIs database
rtcorrection

Correct RT based on a rtmodel.
select

Check matches between chains composition and precursor structures
readFileLipidClasses

Allows reading a CSV that contains lipid classes and adducts to perform annotations and retention time predictions.
setmsbatch

Create msbatch for batch processing.
searchIsotopesmsbatch

Targeted isotopes search for msbatch
rtdevplot

Plot retention time deviation
smdb

SMs database
readMSfile

Read mzXML file and initiate msobject
sumChains

Calculate total number of carbons and double bounds of lipid chains
sphPdb

Sphingoid bases phosphate database
peodb

O-PE database
tgdb

TGs database
sphdb

Sphingoid bases database
removeduplicatedpeaks

Remove duplicated features after grouping step
MassCer

Calculate formula and mass of ceramides
LipidMSapp

LipidMS shiny app
MassCL

Calculate formula and mass of CL
MassLysoPAo

Calculate formula and mass of LPAo
MassAcylCer

Calculate formula and mass of acylceramides
MassLysoPEo

Calculate formula and mass of LPEo
MassLysoPC

Calculate formula and mass of LysoPC
MassFA

Calculate formula and mass of fatty acids
MassCarnitines

Calculate formula and mass of carnitines
MassCerP

Calculate formula and mass of ceramides phosphate
MassDG

Calculate formula and mass of DG
CEdb

CEs database
MassCE

Calculate formula and mass of cholesterol esthers
MassLysoPE

Calculate formula and mass of LPE
MassGlcCer

Calculate formula and mass of glucoceramides
MassLysoPCo

Calculate formula and mass of LysoPCo
MassFAHFA

Calculate formula and mass of FAHFA
MassLysoPCp

Calculate formula and mass of LysoPCp
MassHFA

Calculate formula and mass of hydroxi fatty acids
MassLysoPA

Calculate formula and mass of LPA