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

447

Version

3.1.2

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

December 18th, 2025

Functions in LipidMS (3.1.2)

MassLysoPC

Calculate formula and mass of LysoPC
MassLysoPAo

Calculate formula and mass of LPAo
MassLysoPEp

Calculate formula and mass of LPEp
MassPC

Calculate formula and mass of PC
MassPCo

Calculate formula and mass of PCo
MassPI

Calculate formula and mass of PI
MassPEp

Calculate formula and mass of plasmenyl PE
MassLysoPA

Calculate formula and mass of LPA
MassPS

Calculate formula and mass of PS
MassLysoPEo

Calculate formula and mass of LPEo
MassMG

Calculate formula and mass of MG
MassHFA

Calculate formula and mass of hydroxi fatty acids
MassPIP3

Calculate formula and mass of PIP3
alignmsbatch

Align samples from an msbatch
badb

Bile acids database
MassPA

Calculate formula and mass of PA
MassLysoPG

Calculate formula and mass of LPG
MassPE

Calculate formula and mass of PE
MassLysoPCp

Calculate formula and mass of LysoPCp
MassLysoPCo

Calculate formula and mass of LysoPCo
baconjdb

Bile acids conjugates database
MassPG

Calculate formula and mass of PG
annotateIsotopes

Annotate isotopes
MassPEo

Calculate formula and mass of plasmanyl PE
chains

extract chains composition from a lipid name
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.
MassPCp

Calculate formula and mass of PCp
assignDB

Load LipidMS default data bases
MassGlcCer

Calculate formula and mass of glucoceramides
MassPIP

Calculate formula and mass of PIP
MassLysoPI

Calculate formula and mass of LPI
MassLysoPS

Calculate formula and mass of LysoPS
combineChains

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

Search of chain specific fragments
dataProcessing

Process mzXML files individually: peakpicking and isotope annotation
MassFAHFA

Calculate formula and mass of FAHFA
acylcerdb

AcylCeramides database
clustering

EIC extraction based on previous partitions generated by partitioning
clustdist

Calculate max distance between clusters.
dbFourChains

Creation of a database for C.
annotatemsbatch

Lipid annotation for an msbatch
MassSphP

Calculate formula and mass of sphingoid phosphate bases
MassSph

Calculate formula and mass of sphingoid bases
MassPIP2

Calculate formula and mass of PIP2
cerdb

Ceramides database
carnitinesdb

Carnitines database
cbs

Total number of carbons and double bounds
MassSM

Calculate formula and mass of sphingomyelines
cldb

Cardiolipins database
combineClassesAdducts

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

Fill peaks from a grouped msbatch
MassTG

Calculate formula and mass of TG
filtermsms

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

HFAs database
dbThreeChains

Creation of a database for TG.
fahfadb

FAHFAs database
clust

Clustering for MS peaks based on mz or RT.
dbTwoChains

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

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

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

FAs database
idAcylCerpos

Acylceramides (AcylCer) annotation for ESI+
idAcylCerneg

Acylceramides (AcylCer) annotation for ESI-
filtrateAdducts

Remove low adduct supported candidates to avoid false positives.
checkIntensityRules

Check intensity rules
checkIntRules

Check intensity rules
adductsTable

Adducts table
getfeaturestable

Write features table based on groups
coelutingFrags

Coeluting fragments extraction
crossTables

Cross the original MS1 peaklist with the annotation results
crossAdducts

Cross different candidates tables to remove false positives.
coelutionScore

calculate coelution score between two peaks
cerPdb

Ceramides Phosphate database
ddaFrags

MS/MS scan extraction of a precursor in DDA
dbPlasmalogens

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

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

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

Lysophosphoethanolamines (LPE) annotation for ESI-
idBAneg

Bile Acids (BA) annotation for ESI-
idLPEpos

Lysophosphoethanolamines (LPE) annotation for ESI+
idCerPpos

Ceramides phosphate (CerP) annotation for ESI+
findMS2precursor

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

Lysophosphoserines (LPS) annotation for ESI-
getFormula

Get formula and neutral mass for annotated compounds
dgdb

DGs database
.with_future_plan

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

Obtain an inclusion list from the annotation results
diffcb

Difference between two carbon:bounds structures
getallpeaks

Extract peaks from all msobjects in a msbatch.
idPCpneg

Plasmenyl Phosphocholines (PCp) annotation for ESI-
idCerneg

Ceramides (Cer) annotation for ESI-
idMGpos

Monoacylglycerol (MG) annotation for ESI+
findPrecursor

Find candidate precursor from fullMS function
idPCneg

Phosphocholines (PC) annotation for ESI-
idCerpos

Ceramides (Cer) annotation for ESI+
idPCpos

Phosphocholines (PC) annotation for ESI+
idLPGneg

Lysophosphoglycerols (LPG) annotation for ESI-
idPCppos

Plasmenyl Phosphocholines (PCp) annotation for ESI+
idPEneg

Phosphoethanolamines (PE) annotation for ESI-
idCerPneg

Ceramides phosphate (CerP) annotation for ESI-
idCarpos

Acylcarnitine annotation for ESI+
idLPIneg

Lysophosphoinositols (LPI) annotation for ESI-
idPEoneg

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-
findCandidates

Search of lipid candidates of a certain class
createLipidDB

Customizable lipid DBs creator
confLevels

Confidence Annotation Levels
idLPCneg

Lysophosphocholines (LPC) annotation for ESI-
idDGpos

Diacylglycerols (DG) annotation for ESI+
idSMpos

Sphyngomyelines (SM) annotation for ESI+
lysopaodb

O-LPA database
idSphPneg

Sphingoid bases phosphate (SphP) annotation for ESI-
idCEpos

Cholesteryl Esters (CE) annotation for ESI+
idFAHFAneg

FAHFA annotation for ESI-
lysopcdb

LPCs database
idFAneg

Fatty Acids (FA) annotation for ESI-
idTGpos

Triacylglycerols (TG) annotation for ESI+
idPEopos

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+
idPConeg

Plasmanyl Phosphocholines (PCo) annotation for ESI-
idPGpos

Phosphoglycerols (PG) annotation for ESI+
idPIneg

Phosphoinositols (PI) annotation for ESI-
pcdb

PCs database
idCLneg

Cardiolipines (CL) annotation for ESI-
groupmsbatch

Group features from an msbatch
pcodb

O-PC database
idSphpos

Sphingoid bases (Sph) annotation for ESI-
lysopeodb

O-LPE database
idPEpos

Phosphoethanolamines (PE) annotation for ESI+
idPEpneg

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-
lysopedb

LPEs database
readMSfile

Read mzXML file and initiate msobject
idSphPpos

Sphingoid bases phosphate (SphP) annotation for ESI+
idPSneg

Phosphoserines (PS) annotation for ESI-
idSMneg

Sphingomyelines (SM) annotation for ESI-
idNEG

Lipids annotation for ESI-
mgdb

MGs database
plotticmsbatch

TIC for all samples in a msbatch
idSphneg

Sphingoid bases (Sph) annotation for ESI-
indexrtpart

Index partitions or clusters assigned during alignment.
lysopepdb

P-LPE database
joinAnnotationResults

Summarize annotation results from an msbatch into the features table
mzMatch

mz match withing a vector of mz values
idPCopos

Plasmanyl Phosphocholines (PCo) annotation for ESI+
rtcorrection

Correct RT based on a rtmodel.
idLPCpos

Lysophosphocholines (LPC) annotation for ESI+
ploteicmsbatch

EIC for all samples in a msbatch
rtdevplot

Plot retention time deviation
idPIpos

Phosphoinositols (PI) annotation for ESI+
idPOS

Lipids annotation for ESI+
peakdetection

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

LPSs database
pgdb

PGs database
pcpdb

P-PC database
pepdb

P-PE database
lysopgdb

LPGs database
pedb

PEs database
peodb

O-PE database
lysopidb

LPIs database
sumChains

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

Targeted isotopes search
padb

PAs database
partitioning

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

TGs database
plotLipids

Plot informative peaks for lipid annotation
removeduplicatedpeaks

Remove duplicated features after grouping step
searchIsotopesmsbatch

Targeted isotopes search for msbatch
sphdb

Sphingoid bases database
pidb

PIs database
select

Check matches between chains composition and precursor structures
setmsbatch

Create msbatch for batch processing.
idPGneg

Phosphoglycerols (PG) annotation for ESI-
idPEppos

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+
nlsphdb

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

PSs database
joinfrags

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

LPAs database
organizeResults

Prepare output for LipidMS annotation functions
lysopcodb

O-LPC database
lysopcpdb

P-LPC database
readFileLipidClasses

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

SMs database
sphPdb

Sphingoid bases phosphate database
LipidMSapp

LipidMS shiny app
MassCer

Calculate formula and mass of ceramides
CEdb

CEs database
MassAcylCer

Calculate formula and mass of acylceramides
MassCarnitines

Calculate formula and mass of carnitines
MassDG

Calculate formula and mass of DG
MassLysoPE

Calculate formula and mass of LPE
MassFA

Calculate formula and mass of fatty acids
MassCE

Calculate formula and mass of cholesterol esthers
MassCL

Calculate formula and mass of CL
MassCerP

Calculate formula and mass of ceramides phosphate