Learn R Programming

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:

Copy Link

Version

Install

install.packages('LipidMS')

Monthly Downloads

442

Version

3.1.1

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

November 3rd, 2025

Functions in LipidMS (3.1.1)

MassPG

Calculate formula and mass of PG
MassLysoPCo

Calculate formula and mass of LysoPCo
createLipidDB

Customizable lipid DBs creator
MassSphP

Calculate formula and mass of sphingoid phosphate bases
checkIntRules

Check intensity rules
checkIntensityRules

Check intensity rules
confLevels

Confidence Annotation Levels
baconjdb

Bile acids conjugates database
badb

Bile acids database
MassLysoPS

Calculate formula and mass of LysoPS
MassSM

Calculate formula and mass of sphingomyelines
MassTG

Calculate formula and mass of TG
MassSph

Calculate formula and mass of sphingoid bases
dataProcessing

Process mzXML files individually: peakpicking and isotope annotation
dbFourChains

Creation of a database for C.
crossAdducts

Cross different candidates tables to remove false positives.
MassLysoPCp

Calculate formula and mass of LysoPCp
MassLysoPI

Calculate formula and mass of LPI
alignmsbatch

Align samples from an msbatch
MassPCp

Calculate formula and mass of PCp
cerdb

Ceramides database
annotateIsotopes

Annotate isotopes
MassPI

Calculate formula and mass of PI
MassGlcCer

Calculate formula and mass of glucoceramides
MassMG

Calculate formula and mass of MG
MassPE

Calculate formula and mass of PE
MassPA

Calculate formula and mass of PA
checkClass

Search of class fragments to confirm the lipid class.
combineChains

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

Load LipidMS default data bases
annotatemsbatch

Lipid annotation for an msbatch
chains

extract chains composition from a lipid name
MassPIP

Calculate formula and mass of PIP
MassPIP2

Calculate formula and mass of PIP2
ddaFrags

MS/MS scan extraction of a precursor in DDA
MassLysoPEp

Calculate formula and mass of LPEp
MassLysoPG

Calculate formula and mass of LPG
combineClassesAdducts

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

Cross the original MS1 peaklist with the annotation results
diffcb

Difference between two carbon:bounds structures
.with_future_plan

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

Find candidate precursor from fullMS function
findMS2precursor

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

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

Calculate formula and mass of plasmenyl PE
getInclusionList

Obtain an inclusion list from the annotation results
MassPEo

Calculate formula and mass of plasmanyl PE
dgdb

DGs database
MassPIP3

Calculate formula and mass of PIP3
chainFrags

Search of chain specific fragments
idCerPpos

Ceramides phosphate (CerP) annotation for ESI+
getallpeaks

Extract peaks from all msobjects in a msbatch.
idCerneg

Ceramides (Cer) annotation for ESI-
idCerpos

Ceramides (Cer) annotation for ESI+
idDGpos

Diacylglycerols (DG) annotation for ESI+
idLPEpos

Lysophosphoethanolamines (LPE) annotation for ESI+
idLPEneg

Lysophosphoethanolamines (LPE) annotation for ESI-
cldb

Cardiolipins database
acylcerdb

AcylCeramides database
idCEpos

Cholesteryl Esters (CE) annotation for ESI+
idCLneg

Cardiolipines (CL) annotation for ESI-
idLPGneg

Lysophosphoglycerols (LPG) annotation for ESI-
idLPIneg

Lysophosphoinositols (LPI) annotation for ESI-
adductsTable

Adducts table
cbs

Total number of carbons and double bounds
cerPdb

Ceramides Phosphate database
MassPS

Calculate formula and mass of PS
idPEopos

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+
idPEoneg

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-
clust

Clustering for MS peaks based on mz or RT.
clustering

EIC extraction based on previous partitions generated by partitioning
dbThreeChains

Creation of a database for TG.
idPCpos

Phosphocholines (PC) annotation for ESI+
idPCpneg

Plasmenyl Phosphocholines (PCp) annotation for ESI-
clustdist

Calculate max distance between clusters.
dbSphingolipids

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

Coeluting fragments extraction
coelutionScore

calculate coelution score between two peaks
idNEG

Lipids annotation for ESI-
idPEppos

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+
dbOneChain

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

Carnitines database
idPCneg

Phosphocholines (PC) annotation for ESI-
idPGneg

Phosphoglycerols (PG) annotation for ESI-
fadb

FAs database
groupmsbatch

Group features from an msbatch
findCandidates

Search of lipid candidates of a certain class
idSphPpos

Sphingoid bases phosphate (SphP) annotation for ESI+
idSphneg

Sphingoid bases (Sph) annotation for ESI-
getfeaturestable

Write features table based on groups
filtrateAdducts

Remove low adduct supported candidates to avoid false positives.
dbPlasmalogens

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

Acylcarnitine annotation for ESI+
frags

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

FAHFAs database
idPIpos

Phosphoinositols (PI) annotation for ESI+
idPOS

Lipids annotation for ESI+
dbTwoChains

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

Fill peaks from a grouped msbatch
dbsAdducts

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

Index partitions or clusters assigned during alignment.
joinAnnotationResults

Summarize annotation results from an msbatch into the features table
idAcylCerneg

Acylceramides (AcylCer) annotation for ESI-
idAcylCerpos

Acylceramides (AcylCer) annotation for ESI+
idBAneg

Bile Acids (BA) annotation for ESI-
filtermsms

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

HFAs database
idFAHFAneg

FAHFA annotation for ESI-
idPCopos

Plasmanyl Phosphocholines (PCo) annotation for ESI+
idPSneg

Phosphoserines (PS) annotation for ESI-
idFAneg

Fatty Acids (FA) annotation for ESI-
idPConeg

Plasmanyl Phosphocholines (PCo) annotation for ESI-
getFormula

Get formula and neutral mass for annotated compounds
idSMneg

Sphingomyelines (SM) annotation for ESI-
lysopidb

LPIs database
padb

PAs database
lysopsdb

LPSs database
idSphPneg

Sphingoid bases phosphate (SphP) annotation for ESI-
idSMpos

Sphyngomyelines (SM) annotation for ESI+
idLPCneg

Lysophosphocholines (LPC) annotation for ESI-
lysopedb

LPEs database
organizeResults

Prepare output for LipidMS annotation functions
idTGpos

Triacylglycerols (TG) annotation for ESI+
idSphpos

Sphingoid bases (Sph) annotation for ESI-
pcdb

PCs database
pcodb

O-PC database
nlsphdb

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

O-LPE database
pedb

PEs database
setmsbatch

Create msbatch for batch processing.
idCerPneg

Ceramides phosphate (CerP) annotation for ESI-
lysopcodb

O-LPC database
pepdb

P-PE database
pgdb

PGs database
lysopcpdb

P-LPC database
readMSfile

Read mzXML file and initiate msobject
removeduplicatedpeaks

Remove duplicated features after grouping step
searchIsotopes

Targeted isotopes search
peodb

O-PE database
tgdb

TGs database
select

Check matches between chains composition and precursor structures
searchIsotopesmsbatch

Targeted isotopes search for msbatch
idLPSneg

Lysophosphoserines (LPS) annotation for ESI-
sphdb

Sphingoid bases database
sumChains

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

Phosphoethanolamines (PE) annotation for ESI-
idMGpos

Monoacylglycerol (MG) annotation for ESI+
idPEpos

Phosphoethanolamines (PE) annotation for ESI+
idPCppos

Plasmenyl Phosphocholines (PCp) annotation for ESI+
idPEpneg

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-
idPGpos

Phosphoglycerols (PG) annotation for ESI+
idPIneg

Phosphoinositols (PI) annotation for ESI-
idLPCpos

Lysophosphocholines (LPC) annotation for ESI+
joinfrags

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

P-PC database
lysopadb

LPAs database
lysopaodb

O-LPA database
lysopcdb

LPCs database
lysopgdb

LPGs database
lysopepdb

P-LPE database
plotLipids

Plot informative peaks for lipid annotation
peakdetection

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

PIs database
rtdevplot

Plot retention time deviation
partitioning

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

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

MGs database
psdb

PSs database
rtcorrection

Correct RT based on a rtmodel.
mzMatch

mz match withing a vector of mz values
plotticmsbatch

TIC for all samples in a msbatch
ploteicmsbatch

EIC for all samples in a msbatch
sphPdb

Sphingoid bases phosphate database
smdb

SMs database
MassCerP

Calculate formula and mass of ceramides phosphate
LipidMSapp

LipidMS shiny app
MassFA

Calculate formula and mass of fatty acids
MassCer

Calculate formula and mass of ceramides
MassCL

Calculate formula and mass of CL
MassCE

Calculate formula and mass of cholesterol esthers
CEdb

CEs database
MassCarnitines

Calculate formula and mass of carnitines
MassDG

Calculate formula and mass of DG
MassLysoPE

Calculate formula and mass of LPE
MassHFA

Calculate formula and mass of hydroxi fatty acids
MassLysoPC

Calculate formula and mass of LysoPC
MassLysoPEo

Calculate formula and mass of LPEo
MassFAHFA

Calculate formula and mass of FAHFA
MassLysoPAo

Calculate formula and mass of LPAo
MassAcylCer

Calculate formula and mass of acylceramides
MassLysoPA

Calculate formula and mass of LPA
MassPCo

Calculate formula and mass of PCo
MassPC

Calculate formula and mass of PC