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LipidMS (version 3.0.3)

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

Description

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) .

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Version

Install

install.packages('LipidMS')

Monthly Downloads

327

Version

3.0.3

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

February 22nd, 2022

Functions in LipidMS (3.0.3)

Calculate formula and mass of CL

Calculate formula and mass of ceramides

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of LysoPC

Calculate formula and mass of LPAo

LipidMS shiny app

Calculate formula and mass of LPE

Calculate formula and mass of PC

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LPEp

Calculate formula and mass of PCo

Calculate formula and mass of LPA

Calculate formula and mass of acylceramides

Calculate formula and mass of LysoPCo

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of LysoPCp

Calculate formula and mass of PCp

Calculate formula and mass of sphingomyelines

Calculate formula and mass of PE

Calculate formula and mass of PIP3

Calculate formula and mass of LPEo

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of LPG

Calculate formula and mass of PS

Calculate formula and mass of carnitines

Calculate formula and mass of PIP

Calculate formula and mass of DG

Calculate formula and mass of FAHFA

Calculate formula and mass of LysoPS

Calculate formula and mass of LPI

Calculate formula and mass of fatty acids

Calculate formula and mass of sphingoid phosphate bases

Align samples from an msbatch

annotateIsotopes

Annotate isotopes

Calculate formula and mass of glucoceramides

Check intensity rules

Calculate formula and mass of PIP2

Ceramides database

Calculate formula and mass of sphingoid bases

Calculate formula and mass of MG

annotatemsbatch

Lipid annotation for an msbatch

Load LipidMS default data bases

Calculate formula and mass of PA

Calculate formula and mass of PI

Search of chain specific fragments

Calculate formula and mass of TG

AcylCeramides database

Calculate formula and mass of PG

batchdataProcessing

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

Combine chain fragments that could belong to the same precursor.

Carnitines database

Confidence Annotation Levels

Calculate formula and mass of plasmenyl PE

Calculate max distance between clusters.

Bile acids database

checkIntensityRules

Check intensity rules

Search of lipid candidates of a certain class

Customizable lipid DBs creator

Clustering for MS peaks based on mz or RT.

Ceramides Phosphate database

Bile acids conjugates database

Total number of carbons and double bounds

Cardiolipins database

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

extract chains composition from a lipid name

EIC extraction based on previous partitions generated by partitioning

Creation of a database for TG.

Cross different candidates tables to remove false positives.

Get formula and neutral mass for annotated compounds

Acylceramides (AcylCer) annotation for ESI+

Coeluting fragments extraction

calculate coelution score between two peaks

Search for fragments of interest withing a list of coeluting fragments

Creation of a database for FAHFA, DG and PL.

dbSphingolipids

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

Search of class fragments to confirm the lipid class.

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

Creation of a database for C.

Bile Acids (BA) annotation for ESI-

Lysophosphoglycerols (LPG) annotation for ESI-

Cholesteryl Esters (CE) annotation for ESI+

Acylcarnitine annotation for ESI+

Cardiolipines (CL) annotation for ESI-

Ceramides phosphate (CerP) annotation for ESI-

Lipids annotation for ESI-

Cross the original MS1 peaklist with the annotation results

Phosphocholines (PC) annotation for ESI-

findMS2precursor

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

Lysophosphoinositols (LPI) annotation for ESI-

MS/MS scan extraction of a precursor in DDA

Difference between two carbon:bounds structures

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

FAHFAs database

Acylceramides (AcylCer) annotation for ESI-

Ceramides phosphate (CerP) annotation for ESI+

Find candidate precursor from fullMS function

Ceramides (Cer) annotation for ESI-

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Lysophosphoserines (LPS) annotation for ESI-

fillpeaksmsbatch

Fill peaks from a grouped msbatch

Sphingoid bases phosphate (SphP) annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Extract peaks from all msobjects in a msbatch.

getInclusionList

Obtain an inclusion list from the annotation results

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

Fatty Acids (FA) annotation for ESI-

FAHFA annotation for ESI-

Sphyngomyelines (SM) annotation for ESI+

Sphingoid bases phosphate (SphP) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

Ceramides (Cer) annotation for ESI+

Monoacylglycerol (MG) annotation for ESI+

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

Diacylglycerols (DG) annotation for ESI+

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

mz match withing a vector of mz values

EIC for all samples in a msbatch

Group features from an msbatch

Process mzXML files individually: peakpicking and isotope annotation

getfeaturestable

Write features table based on groups

Lysophosphoethanolamines (LPE) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI-

TIC for all samples in a msbatch

Check matches between chains composition and precursor structures

Phosphoglycerols (PG) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI-

Plasmenyl Phosphocholines (PCp) annotation for ESI+

Plasmenyl Phosphocholines (PCp) annotation for ESI-

Index partitions or clusters assigned during alignment.

Phosphocholines (PC) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI+

joinAnnotationResults

Summarize annotation results from an msbatch into the features table

Plot informative peaks for lipid annotation

Targeted isotopes search

searchIsotopesmsbatch

Targeted isotopes search for msbatch

Phosphoinositols (PI) annotation for ESI-

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

Sphingomyelines (SM) annotation for ESI-

Phosphoserines (PS) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI+

Sphingoid bases phosphate database

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI-

Phosphoinositols (PI) annotation for ESI+

Create msbatch for batch processing.

Lipids annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

organizeResults

Prepare output for LipidMS annotation functions

Triacylglycerols (TG) annotation for ESI+

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

Plot retention time deviation

Sphingoid bases database

Correct RT based on a rtmodel.

Calculate total number of carbons and double bounds of lipid chains

peak-pick based on previous EIC clusters generated by clustering

Read mzXML file and initiate msobject