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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

388

Version

3.0.5

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

May 27th, 2024

Functions in LipidMS (3.0.5)

Calculate formula and mass of LPE

Calculate formula and mass of ceramides

Calculate formula and mass of ceramides phosphate

Check intensity rules

LipidMS shiny app

Calculate formula and mass of DG

Calculate formula and mass of LPEp

Calculate formula and mass of FAHFA

Calculate formula and mass of fatty acids

batchdataProcessing

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

Calculate formula and mass of CL

Calculate formula and mass of PE

Calculate formula and mass of glucoceramides

Phosphocholines (PC) annotation for ESI-

Calculate formula and mass of sphingoid bases

Calculate formula and mass of LysoPCo

Calculate formula and mass of PI

Coeluting fragments extraction

Calculate formula and mass of LPEo

Calculate formula and mass of sphingomyelines

Align samples from an msbatch

annotateIsotopes

Annotate isotopes

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of PIP

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Calculate formula and mass of carnitines

Calculate formula and mass of LPI

Ceramides (Cer) annotation for ESI-

Calculate formula and mass of plasmanyl PE

Carnitines database

checkIntensityRules

Check intensity rules

Phosphocholines (PC) annotation for ESI+

Clustering for MS peaks based on mz or RT.

Calculate formula and mass of PC

Calculate formula and mass of LysoPCp

Calculate formula and mass of LPG

Cross the original MS1 peaklist with the annotation results

Calculate formula and mass of LPAo

Calculate formula and mass of cholesterol esthers

Creation of a database for FAHFA, DG and PL.

Calculate formula and mass of acylceramides

Calculate formula and mass of MG

Process mzXML files individually: peakpicking and isotope annotation

Creation of a database for TG.

Acylceramides (AcylCer) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Cardiolipins database

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LPA

Calculate formula and mass of plasmenyl PE

Sphingomyelines (SM) annotation for ESI-

Calculate formula and mass of LysoPC

Calculate formula and mass of PA

Search of class fragments to confirm the lipid class.

Combine chain fragments that could belong to the same precursor.

Search of lipid candidates of a certain class

Phosphoethanolamines (PE) annotation for ESI-

Phosphoinositols (PI) annotation for ESI-

Acylcarnitine annotation for ESI+

getInclusionList

Obtain an inclusion list from the annotation results

AcylCeramides database

Total number of carbons and double bounds

Calculate formula and mass of PCo

Calculate formula and mass of PCp

Lipids annotation for ESI-

Calculate formula and mass of LysoPS

Search for fragments of interest withing a list of coeluting fragments

Sphingoid bases phosphate (SphP) annotation for ESI-

Index partitions or clusters assigned during alignment.

Extract peaks from all msobjects in a msbatch.

FAHFA annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

calculate coelution score between two peaks

Calculate formula and mass of PIP3

Plasmenyl Phosphocholines (PCp) annotation for ESI-

Ceramides phosphate (CerP) annotation for ESI-

Customizable lipid DBs creator

Calculate formula and mass of TG

Calculate formula and mass of PG

Calculate formula and mass of PIP2

Calculate max distance between clusters.

Bile acids conjugates database

Creation of a database for C.

Bile acids database

Sphingoid bases (Sph) annotation for ESI-

extract chains composition from a lipid name

Phosphoserines (PS) annotation for ESI-

Cross different candidates tables to remove false positives.

Find candidate precursor from fullMS function

Calculate formula and mass of PS

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

Confidence Annotation Levels

Difference between two carbon:bounds structures

MS/MS scan extraction of a precursor in DDA

Get formula and neutral mass for annotated compounds

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

Fatty Acids (FA) annotation for ESI-

annotatemsbatch

Lipid annotation for an msbatch

dbSphingolipids

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

fillpeaksmsbatch

Fill peaks from a grouped msbatch

findMS2precursor

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

TIC for all samples in a msbatch

Ceramides database

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Sphingoid bases database

Load LipidMS default data bases

Ceramides Phosphate database

Correct RT based on a rtmodel.

Search of chain specific fragments

Lysophosphoserines (LPS) annotation for ESI-

Ceramides phosphate (CerP) annotation for ESI+

Acylceramides (AcylCer) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

FAHFAs database

Cardiolipines (CL) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Phosphoinositols (PI) annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Group features from an msbatch

organizeResults

Prepare output for LipidMS annotation functions

EIC extraction based on previous partitions generated by partitioning

Bile Acids (BA) annotation for ESI-

Monoacylglycerol (MG) annotation for ESI+

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

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

Triacylglycerols (TG) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI+

Lysophosphoinositols (LPI) annotation for ESI-

Plasmenyl Phosphocholines (PCp) annotation for ESI+

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

getfeaturestable

Write features table based on groups

Lipids annotation for ESI+

mz match withing a vector of mz values

Ceramides (Cer) annotation for ESI+

Plot informative peaks for lipid annotation

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

Sphyngomyelines (SM) annotation for ESI+

Calculate total number of carbons and double bounds of lipid chains

Cholesteryl Esters (CE) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

EIC for all samples in a msbatch

Lysophosphocholines (LPC) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI-

Diacylglycerols (DG) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

joinAnnotationResults

Summarize annotation results from an msbatch into the features table

Plot retention time deviation

peak-pick based on previous EIC clusters generated by clustering

Targeted isotopes search

Sphingoid bases phosphate database

Read mzXML file and initiate msobject

searchIsotopesmsbatch

Targeted isotopes search for msbatch

Check matches between chains composition and precursor structures

Create msbatch for batch processing.