Package: LipidMS 3.1.3

LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.

Authors:M Isabel Alcoriza-Balaguer [aut, cre], Celia Regal-Marques [aut]

LipidMS_3.1.3.tar.gz
LipidMS_3.1.3.zip(r-4.7)LipidMS_3.1.3.zip(r-4.6)LipidMS_3.1.3.zip(r-4.5)
LipidMS_3.1.3.tgz(r-4.6-x86_64)LipidMS_3.1.3.tgz(r-4.6-arm64)LipidMS_3.1.3.tgz(r-4.5-x86_64)LipidMS_3.1.3.tgz(r-4.5-arm64)
LipidMS_3.1.3.tar.gz(r-4.7-arm64)LipidMS_3.1.3.tar.gz(r-4.7-x86_64)LipidMS_3.1.3.tar.gz(r-4.6-arm64)LipidMS_3.1.3.tar.gz(r-4.6-x86_64)
LipidMS_3.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LipidMS/json (API)

# Install 'LipidMS' in R:

install.packages('LipidMS', repos = c('https://maialba3.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/maialba3/lipidms/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

acylcerdb - AcylCeramides database
adductsTable - Adducts table
baconjdb - Bile acids conjugates database
badb - Bile acids database
carnitinedb - Carnitine database
CEdb - CEs database
cerdb - Ceramides database
cerPdb - Ceramides Phosphate database
cldb - Cardiolipins database
confLevels - Confidence Annotation Levels
dgdb - DGs database
fadb - FAs database
fahfadb - FAHFAs database
hfadb - HFAs database
lysopadb - LPAs database
lysopaodb - O-LPA database
lysopcdb - LPCs database
lysopcodb - O-LPC database
lysopcpdb - P-LPC database
lysopedb - LPEs database
lysopeodb - O-LPE database
lysopepdb - P-LPE database
lysopgdb - LPGs database
lysopidb - LPIs database
lysopsdb - LPSs database
mgdb - MGs database
nlsphdb - Neutral losses db for sphingoid bases. It is employed by idCerneg function.
padb - PAs database
pcdb - PCs database
pcodb - O-PC database
pcpdb - P-PC database
pedb - PEs database
peodb - O-PE database
pepdb - P-PE database
pgdb - PGs database
pidb - PIs database
psdb - PSs database
smdb - SMs database
sphdb - Sphingoid bases database
sphPdb - Sphingoid bases phosphate database
tgdb - TGs database

On CRAN:

cpp

5.10 score 2 stars 1 packages 14 scripts 386 downloads 3 mentions 73 exports 61 dependencies

Last updated from:e5960e3ba2. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	205
linux-devel-x86_64	OK	237
source / vignettes	OK	234
linux-release-arm64	OK	191
linux-release-x86_64	OK	242
macos-release-arm64	OK	124
macos-release-x86_64	OK	248
macos-oldrel-arm64	OK	106
macos-oldrel-x86_64	OK	250
windows-devel	OK	146
windows-release	OK	160
windows-oldrel	OK	172
wasm-release	OK	174

Exports:alignmsbatch annotatemsbatch assignDB batchdataProcessing chainFrags checkClass checkIntensityRules coelutingFrags combineChains createLipidDB crossTables dataProcessing ddaFrags fillpeaksmsbatch findCandidates getInclusionList groupmsbatch idAcylCerneg idAcylCerpos idBAneg idCarpos idCEpos idCerneg idCerPneg idCerpos idCerPpos idCLneg idDGpos idFAHFAneg idFAneg idLPCneg idLPCpos idLPEneg idLPEpos idLPGneg idLPIneg idLPSneg idMGpos idNEG idPCneg idPConeg idPCopos idPCpneg idPCpos idPCppos idPEneg idPEoneg idPEopos idPEpneg idPEpos idPEppos idPGneg idPGpos idPIneg idPIpos idPOS idPSneg idSMneg idSMpos idSphneg idSphPneg idSphpos idSphPpos idTGpos LipidMSapp organizeResults ploteicmsbatch plotLipids plotticmsbatch rtdevplot searchIsotopes searchIsotopesmsbatch setmsbatch

Dependencies:base64enc bslib cachem CHNOSZ cli codetools cpp11 crosstalk digest DT evaluate farver fastmap fontawesome fs future future.apply ggplot2 globals glue gtable highr htmltools htmlwidgets isoband iterators jquerylib jsonlite knitr labeling later lazyeval lifecycle listenv magrittr memoise mime otel parallelly patchwork promises R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp readMzXmlData rlang rmarkdown S7 sass scales tinytex vctrs viridisLite withr xfun XML yaml

LipidMS workflow

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2026-03-23
Started: 2021-01-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AcylCeramides database	acylcerdb
Adducts table	adductsTable
Align samples from an msbatch	alignmsbatch
Lipid annotation for an msbatch	annotatemsbatch
Load LipidMS default data bases	assignDB
Bile acids conjugates database	baconjdb
Bile acids database	badb
Process several mzXML files (peakpicking and isotope annotation) and create an msbatch for batch processing.	batchdataProcessing
Carnitine database	carnitinedb
CEs database	CEdb
Ceramides database	cerdb
Ceramides Phosphate database	cerPdb
Search of chain specific fragments	chainFrags
Search of class fragments to confirm the lipid class.	checkClass
Check intensity rules	checkIntensityRules
Cardiolipins database	cldb
Coeluting fragments extraction	coelutingFrags
calculate coelution score between two peaks	coelutionScore
Combine chain fragments that could belong to the same precursor.	combineChains
Confidence Annotation Levels	confLevels
Customizable lipid DBs creator	createLipidDB
Cross the original MS1 peaklist with the annotation results	crossTables
Process mzXML files individually: peakpicking and isotope annotation	dataProcessing
MS/MS scan extraction of a precursor in DDA	ddaFrags
DGs database	dgdb
FAs database	fadb
FAHFAs database	fahfadb
Fill peaks from a grouped msbatch	fillpeaksmsbatch
Search of lipid candidates of a certain class	findCandidates
Obtain an inclusion list from the annotation results	getInclusionList
Group features from an msbatch	groupmsbatch
HFAs database	hfadb
Acylceramides (AcylCer) annotation for ESI-	idAcylCerneg
Acylceramides (AcylCer) annotation for ESI+	idAcylCerpos
Bile Acids (BA) annotation for ESI-	idBAneg
Acylcarnitine annotation for ESI+	idCarpos
Cholesteryl Esters (CE) annotation for ESI+	idCEpos
Ceramides (Cer) annotation for ESI-	idCerneg
Ceramides phosphate (CerP) annotation for ESI-	idCerPneg
Ceramides (Cer) annotation for ESI+	idCerpos
Ceramides phosphate (CerP) annotation for ESI+	idCerPpos
Cardiolipines (CL) annotation for ESI-	idCLneg
Diacylglycerols (DG) annotation for ESI+	idDGpos
FAHFA annotation for ESI-	idFAHFAneg
Fatty Acids (FA) annotation for ESI-	idFAneg
Lysophosphocholines (LPC) annotation for ESI-	idLPCneg
Lysophosphocholines (LPC) annotation for ESI+	idLPCpos
Lysophosphoethanolamines (LPE) annotation for ESI-	idLPEneg
Lysophosphoethanolamines (LPE) annotation for ESI+	idLPEpos
Lysophosphoglycerols (LPG) annotation for ESI-	idLPGneg
Lysophosphoinositols (LPI) annotation for ESI-	idLPIneg
Lysophosphoserines (LPS) annotation for ESI-	idLPSneg
Monoacylglycerol (MG) annotation for ESI+	idMGpos
Lipids annotation for ESI-	idNEG
Phosphocholines (PC) annotation for ESI-	idPCneg
Plasmanyl Phosphocholines (PCo) annotation for ESI-	idPConeg
Plasmanyl Phosphocholines (PCo) annotation for ESI+	idPCopos
Plasmenyl Phosphocholines (PCp) annotation for ESI-	idPCpneg
Phosphocholines (PC) annotation for ESI+	idPCpos
Plasmenyl Phosphocholines (PCp) annotation for ESI+	idPCppos
Phosphoethanolamines (PE) annotation for ESI-	idPEneg
Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-	idPEoneg
Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+	idPEopos
Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-	idPEpneg
Phosphoethanolamines (PE) annotation for ESI+	idPEpos
Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+	idPEppos
Phosphoglycerols (PG) annotation for ESI-	idPGneg
Phosphoglycerols (PG) annotation for ESI+	idPGpos
Phosphoinositols (PI) annotation for ESI-	idPIneg
Phosphoinositols (PI) annotation for ESI+	idPIpos
Lipids annotation for ESI+	idPOS
Phosphoserines (PS) annotation for ESI-	idPSneg
Sphingomyelines (SM) annotation for ESI-	idSMneg
Sphyngomyelines (SM) annotation for ESI+	idSMpos
Sphingoid bases (Sph) annotation for ESI-	idSphneg
Sphingoid bases phosphate (SphP) annotation for ESI-	idSphPneg
Sphingoid bases (Sph) annotation for ESI-	idSphpos
Sphingoid bases phosphate (SphP) annotation for ESI+	idSphPpos
Triacylglycerols (TG) annotation for ESI+	idTGpos
LipidMS shiny app	LipidMSapp
LPAs database	lysopadb
O-LPA database	lysopaodb
LPCs database	lysopcdb
O-LPC database	lysopcodb
P-LPC database	lysopcpdb
LPEs database	lysopedb
O-LPE database	lysopeodb
P-LPE database	lysopepdb
LPGs database	lysopgdb
LPIs database	lysopidb
LPSs database	lysopsdb
MGs database	mgdb
Neutral losses db for sphingoid bases. It is employed by idCerneg function.	nlsphdb
Prepare output for LipidMS annotation functions	organizeResults
PAs database	padb
PCs database	pcdb
O-PC database	pcodb
P-PC database	pcpdb
PEs database	pedb
O-PE database	peodb
P-PE database	pepdb
PGs database	pgdb
PIs database	pidb
EIC for all samples in a msbatch	ploteicmsbatch
Plot informative peaks for lipid annotation	plotLipids
TIC for all samples in a msbatch	plotticmsbatch
PSs database	psdb
Plot retention time deviation	rtdevplot
Targeted isotopes search	searchIsotopes
Targeted isotopes search for msbatch	searchIsotopesmsbatch
Create msbatch for batch processing.	setmsbatch
SMs database	smdb
Sphingoid bases database	sphdb
Sphingoid bases phosphate database	sphPdb
TGs database	tgdb