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LipidMS (version 3.0.2)

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

447

Version

3.0.2

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

January 17th, 2022

Functions in LipidMS (3.0.2)

LipidMS shiny app

Calculate formula and mass of fatty acids

Calculate formula and mass of ceramides

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of DG

Calculate formula and mass of acylceramides

Calculate formula and mass of CL

Calculate formula and mass of FAHFA

Calculate formula and mass of carnitines

Calculate formula and mass of glucoceramides

Calculate formula and mass of PC

Calculate formula and mass of LPI

Calculate formula and mass of PA

Calculate formula and mass of PIP3

Calculate formula and mass of MG

Calculate formula and mass of LysoPC

Calculate formula and mass of LPAo

Calculate formula and mass of PCo

Calculate formula and mass of TG

Calculate formula and mass of PS

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of LysoPS

Calculate formula and mass of sphingomyelines

Total number of carbons and double bounds

Search of chain specific fragments

Cardiolipins database

Clustering for MS peaks based on mz or RT.

AcylCeramides database

Calculate formula and mass of sphingoid bases

Ceramides database

Ceramides Phosphate database

dbSphingolipids

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

Creation of a database for TG.

batchdataProcessing

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

Calculate formula and mass of hydroxi fatty acids

Creation of a database for FAHFA, DG and PL.

Cross the original MS1 peaklist with the annotation results

Combine chain fragments that could belong to the same precursor.

Confidence Annotation Levels

Calculate formula and mass of LPA

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of ceramides phosphate

Carnitines database

Calculate formula and mass of PCp

Calculate formula and mass of PE

Calculate formula and mass of LysoPCo

Process mzXML files individually: peakpicking and isotope annotation

Acylceramides (AcylCer) annotation for ESI-

Calculate formula and mass of plasmenyl PE

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

MS/MS scan extraction of a precursor in DDA

Acylceramides (AcylCer) annotation for ESI+

Search of lipid candidates of a certain class

Bile Acids (BA) annotation for ESI-

Calculate formula and mass of PG

Calculate formula and mass of LysoPCp

Calculate formula and mass of PI

Lysophosphocholines (LPC) annotation for ESI+

Lysophosphocholines (LPC) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI-

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

Calculate formula and mass of LPE

Lysophosphoserines (LPS) annotation for ESI-

Bile acids conjugates database

Bile acids database

Customizable lipid DBs creator

Monoacylglycerol (MG) annotation for ESI+

Cross different candidates tables to remove false positives.

Load LipidMS default data bases

Search of class fragments to confirm the lipid class.

annotatemsbatch

Lipid annotation for an msbatch

extract chains composition from a lipid name

Calculate formula and mass of LPEo

Calculate formula and mass of LPEp

Calculate formula and mass of LPG

Calculate max distance between clusters.

EIC extraction based on previous partitions generated by partitioning

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

getInclusionList

Obtain an inclusion list from the annotation results

Plasmenyl Phosphocholines (PCp) annotation for ESI+

Extract peaks from all msobjects in a msbatch.

FAHFAs database

Calculate formula and mass of PIP

Align samples from an msbatch

checkIntensityRules

Check intensity rules

Check intensity rules

annotateIsotopes

Annotate isotopes

Calculate formula and mass of PIP2

Acylcarnitine annotation for ESI+

Create msbatch for batch processing.

Check matches between chains composition and precursor structures

Ceramides phosphate (CerP) annotation for ESI-

Coeluting fragments extraction

calculate coelution score between two peaks

findMS2precursor

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

Phosphoethanolamines (PE) annotation for ESI-

Group features from an msbatch

Difference between two carbon:bounds structures

getfeaturestable

Write features table based on groups

Find candidate precursor from fullMS function

Sphingoid bases (Sph) annotation for ESI-

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

FAHFA annotation for ESI-

Search for fragments of interest withing a list of coeluting fragments

Creation of a database for C.

Get formula and neutral mass for annotated compounds

fillpeaksmsbatch

Fill peaks from a grouped msbatch

Lipids annotation for ESI+

Phosphoserines (PS) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Cardiolipines (CL) annotation for ESI-

Cholesteryl Esters (CE) annotation for ESI+

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

Ceramides (Cer) annotation for ESI+

Lipids annotation for ESI-

Diacylglycerols (DG) annotation for ESI+

Plasmanyl Phosphocholines (PCo) annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Phosphocholines (PC) annotation for ESI-

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Ceramides phosphate (CerP) annotation for ESI+

Sphingoid bases database

Sphingoid bases (Sph) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

Ceramides (Cer) annotation for ESI-

Lysophosphoglycerols (LPG) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

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

Phosphoglycerols (PG) annotation for ESI+

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

Phosphoinositols (PI) annotation for ESI-

Plasmenyl Phosphocholines (PCp) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Calculate total number of carbons and double bounds of lipid chains

Phosphocholines (PC) annotation for ESI+

Sphyngomyelines (SM) annotation for ESI+

Plot retention time deviation

organizeResults

Prepare output for LipidMS annotation functions

Correct RT based on a rtmodel.

Sphingoid bases phosphate (SphP) annotation for ESI-

Index partitions or clusters assigned during alignment.

joinAnnotationResults

Summarize annotation results from an msbatch into the features table

Plot informative peaks for lipid annotation

Read mzXML file and initiate msobject

mz match withing a vector of mz values

EIC for all samples in a msbatch

TIC for all samples in a msbatch

Targeted isotopes search

peak-pick based on previous EIC clusters generated by clustering

searchIsotopesmsbatch

Targeted isotopes search for msbatch

Sphingoid bases phosphate database