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LipidMS (version 3.0.0)

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

3.0.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

May 25th, 2021

Functions in LipidMS (3.0.0)

Calculate formula and mass of CL

LipidMS shiny app

Calculate formula and mass of acylceramides

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of ceramides

Calculate formula and mass of DG

Calculate formula and mass of fatty acids

Calculate formula and mass of carnitines

Calculate formula and mass of LysoPCo

Calculate formula and mass of LPE

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of LPI

Calculate formula and mass of LysoPS

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LysoPCp

Calculate formula and mass of PS

Calculate formula and mass of PIP3

Calculate formula and mass of LPA

Calculate formula and mass of PE

Calculate formula and mass of PIP

Calculate formula and mass of PCp

Calculate formula and mass of sphingoid phosphate bases

Total number of carbons and double bounds

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of PIP2

Ceramides Phosphate database

Calculate formula and mass of TG

Align samples from an msbatch

Calculate formula and mass of LPAo

Calculate formula and mass of LysoPC

Calculate formula and mass of PC

Calculate formula and mass of PCo

Calculate formula and mass of LPEo

Calculate formula and mass of LPEp

checkIntensityRules

Check intensity rules

Check intensity rules

annotateIsotopes

Annotate isotopes

Combine chain fragments that could belong to the same precursor.

Calculate formula and mass of LPG

AcylCeramides database

Coeluting fragments extraction

Search of class fragments to confirm the lipid class.

Cardiolipins database

Calculate formula and mass of sphingomyelines

extract chains composition from a lipid name

Clustering for MS peaks based on mz or RT.

MS/MS scan extraction of a precursor in DDA

Creation of a database for FAHFA, DG and PL.

Calculate formula and mass of MG

Confidence Annotation Levels

Calculate formula and mass of glucoceramides

Creation of a database for TG.

Calculate formula and mass of FAHFA

Calculate formula and mass of PA

Acylceramides (AcylCer) annotation for ESI+

dbSphingolipids

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

calculate coelution score between two peaks

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

Creation of a database for C.

Calculate formula and mass of sphingoid bases

Bile acids conjugates database

Find candidate precursor from fullMS function

Ceramides database

Bile acids database

Search of chain specific fragments

findMS2precursor

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

getfeaturestable

Write features table based on groups

Ceramides phosphate (CerP) annotation for ESI+

Group features from an msbatch

Calculate formula and mass of PG

Ceramides (Cer) annotation for ESI-

Calculate formula and mass of PI

Load LipidMS default data bases

annotatemsbatch

Lipid annotation for an msbatch

batchdataProcessing

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

Lysophosphoglycerols (LPG) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Carnitines database

Calculate max distance between clusters.

Acylcarnitine annotation for ESI+

Bile Acids (BA) annotation for ESI-

Cross the original MS1 peaklist with the annotation results

Customizable lipid DBs creator

Process mzXML files individually: peakpicking and isotope annotation

Cross different candidates tables to remove false positives.

Search for fragments of interest withing a list of coeluting fragments

EIC extraction based on previous partitions generated by partitioning

Ceramides phosphate (CerP) annotation for ESI-

FAHFAs database

getInclusionList

Obtain an inclusion list from the annotation results

Cholesteryl Esters (CE) annotation for ESI+

Search of lipid candidates of a certain class

Lipids annotation for ESI-

Cardiolipines (CL) annotation for ESI-

Difference between two carbon:bounds structures

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Get formula and neutral mass for annotated compounds

Plasmanyl Phosphocholines (PCo) annotation for ESI-

fillpeaksmsbatch

Fill peaks from a grouped msbatch

Lysophosphocholines (LPC) annotation for ESI-

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

Lysophosphocholines (LPC) annotation for ESI+

Extract peaks from all msobjects in a msbatch.

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

Acylceramides (AcylCer) annotation for ESI-

Plasmenyl Phosphocholines (PCp) annotation for ESI+

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

Diacylglycerols (DG) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI-

Ceramides (Cer) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Fatty Acids (FA) annotation for ESI-

FAHFA annotation for ESI-

Sphingoid bases (Sph) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

Phosphocholines (PC) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

Sphyngomyelines (SM) annotation for ESI+

Index partitions or clusters assigned during alignment.

Monoacylglycerol (MG) annotation for ESI+

Lysophosphoserines (LPS) annotation for ESI-

Targeted isotopes search

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

Plasmenyl Phosphocholines (PCp) annotation for ESI-

peak-pick based on previous EIC clusters generated by clustering

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

Phosphocholines (PC) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

searchIsotopesmsbatch

Targeted isotopes search for msbatch

organizeResults

Prepare output for LipidMS annotation functions

joinAnnotationResults

Summarize annotation results from an msbatch into the features table

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

Correct RT based on a rtmodel.

Plot retention time deviation

Phosphoglycerols (PG) annotation for ESI+

Sphingoid bases phosphate database

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Lipids annotation for ESI+

Plot informative peaks for lipid annotation

Phosphoserines (PS) annotation for ESI-

EIC for all samples in a msbatch

Check matches between chains composition and precursor structures

Create msbatch for batch processing.

Calculate total number of carbons and double bounds of lipid chains

Sphingoid bases database

TIC for all samples in a msbatch

Phosphoinositols (PI) annotation for ESI-

Read mzXML file and initiate msobject

mz match withing a vector of mz values