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LipidMS v3.0

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

Batch processing: peak-picking, grouping and alignment wrapped in batchdataProcessing(). Lipid annotation for msbatch objects simplified with annotatemsbatch().
New lipid classes: plasmanyl and plasmenyl PC and PE, acylceramides and ceramides phosphate.
GUI through shiny app running LipidMSapp().
Improved graphical outputs for lipid annotation.

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. bioRxiv, 2022. doi.org/10.1101/2022.02.25.476005

References:

Peak-picking algorithm has been imported from enviPick R-package (Martin Loos) (https://CRAN.R-project.org/package=enviPick)

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Version

Install

install.packages('LipidMS')

Monthly Downloads

321

Version

3.0.4

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

February 19th, 2024

Functions in LipidMS (3.0.4)

Calculate formula and mass of LPE

Calculate formula and mass of LPEo

Calculate formula and mass of PC

Calculate formula and mass of glucoceramides

Calculate formula and mass of PIP2

Check intensity rules

checkIntensityRules

Check intensity rules

Calculate formula and mass of LysoPC

Calculate formula and mass of PIP

Calculate formula and mass of TG

Calculate formula and mass of LPEp

Search of chain specific fragments

Calculate formula and mass of LPG

Combine chain fragments that could belong to the same precursor.

Calculate formula and mass of sphingomyelines

Calculate formula and mass of MG

Ceramides database

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of PCo

Calculate formula and mass of LPAo

Calculate formula and mass of PG

Calculate formula and mass of PA

Calculate formula and mass of PIP3

AcylCeramides database

Calculate formula and mass of PS

calculate coelution score between two peaks

Coeluting fragments extraction

Calculate formula and mass of PI

annotatemsbatch

Lipid annotation for an msbatch

Bile Acids (BA) annotation for ESI-

Load LipidMS default data bases

Clustering for MS peaks based on mz or RT.

Calculate formula and mass of PE

Calculate formula and mass of PCp

Cardiolipins database

Confidence Annotation Levels

Acylceramides (AcylCer) annotation for ESI+

Search of class fragments to confirm the lipid class.

Bile acids conjugates database

extract chains composition from a lipid name

Bile acids database

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of sphingoid bases

Calculate formula and mass of plasmanyl PE

Process mzXML files individually: peakpicking and isotope annotation

batchdataProcessing

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

Cross the original MS1 peaklist with the annotation results

Customizable lipid DBs creator

Align samples from an msbatch

Difference between two carbon:bounds structures

Search for fragments of interest withing a list of coeluting fragments

annotateIsotopes

Annotate isotopes

Total number of carbons and double bounds

Calculate max distance between clusters.

Get formula and neutral mass for annotated compounds

Lipids annotation for ESI-

Phosphocholines (PC) annotation for ESI-

dbSphingolipids

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

EIC extraction based on previous partitions generated by partitioning

Creation of a database for C.

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

Ceramides Phosphate database

Cross different candidates tables to remove false positives.

Plasmenyl Phosphocholines (PCp) annotation for ESI-

findMS2precursor

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

getfeaturestable

Write features table based on groups

Find candidate precursor from fullMS function

Carnitines database

getInclusionList

Obtain an inclusion list from the annotation results

FAHFAs database

Extract peaks from all msobjects in a msbatch.

Phosphoglycerols (PG) annotation for ESI+

Ceramides phosphate (CerP) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI-

Phosphocholines (PC) annotation for ESI+

Phosphoinositols (PI) annotation for ESI-

Creation of a database for FAHFA, DG and PL.

Ceramides (Cer) annotation for ESI-

Acylceramides (AcylCer) annotation for ESI-

Ceramides (Cer) annotation for ESI+

MS/MS scan extraction of a precursor in DDA

Diacylglycerols (DG) annotation for ESI+

Creation of a database for TG.

joinAnnotationResults

Summarize annotation results from an msbatch into the features table

Lysophosphoethanolamines (LPE) annotation for ESI+

Index partitions or clusters assigned during alignment.

Group features from an msbatch

fillpeaksmsbatch

Fill peaks from a grouped msbatch

Phosphoglycerols (PG) annotation for ESI-

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

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

Phosphoserines (PS) annotation for ESI-

Targeted isotopes search

searchIsotopesmsbatch

Targeted isotopes search for msbatch

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Sphingomyelines (SM) annotation for ESI-

Create msbatch for batch processing.

Search of lipid candidates of a certain class

Cholesteryl Esters (CE) annotation for ESI+

Lysophosphocholines (LPC) annotation for ESI+

Lysophosphoserines (LPS) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Check matches between chains composition and precursor structures

Read mzXML file and initiate msobject

Ceramides phosphate (CerP) annotation for ESI-

organizeResults

Prepare output for LipidMS annotation functions

Cardiolipines (CL) annotation for ESI-

Acylcarnitine annotation for ESI+

Monoacylglycerol (MG) annotation for ESI+

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

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

Sphingoid bases phosphate (SphP) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI-

FAHFA annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Plasmenyl Phosphocholines (PCp) annotation for ESI+

Lysophosphoinositols (LPI) annotation for ESI-

Sphingoid bases (Sph) annotation for ESI-

Plot informative peaks for lipid annotation

Sphingoid bases database

Calculate total number of carbons and double bounds of lipid chains

Triacylglycerols (TG) annotation for ESI+

Sphingoid bases phosphate (SphP) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

mz match withing a vector of mz values

peak-pick based on previous EIC clusters generated by clustering

Sphyngomyelines (SM) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Lipids annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI-

Phosphoinositols (PI) annotation for ESI+

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

Plot retention time deviation

Correct RT based on a rtmodel.

TIC for all samples in a msbatch

EIC for all samples in a msbatch

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

Sphingoid bases phosphate database

Calculate formula and mass of CL

LipidMS shiny app

Calculate formula and mass of carnitines

Calculate formula and mass of acylceramides

Calculate formula and mass of DG

Calculate formula and mass of ceramides

Calculate formula and mass of LysoPCo

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of LysoPCp

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of fatty acids

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LPA

Calculate formula and mass of FAHFA

Calculate formula and mass of LysoPS

Calculate formula and mass of LPI