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LipidMS (version 2.0.0)

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

Description

Lipid annotation in untargeted liquid chromatography mass spectrometry 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

282

Version

2.0.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

January 19th, 2021

Functions in LipidMS (2.0.0)

Calculate formula and mass of fatty acids

LipidMS shiny app

Calculate formula and mass of carnitines

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of DG

Calculate formula and mass of ceramides

Calculate formula and mass of FAHFA

Calculate formula and mass of CL

Calculate formula and mass of glucoceramides

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LPA

Calculate formula and mass of PE

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of LysoPC

Calculate formula and mass of LysoPCp

Calculate formula and mass of LPE

Calculate formula and mass of LPEo

Calculate formula and mass of sphingoid bases

Calculate formula and mass of PA

Load LipidMS default data bases

Search of class fragments to confirm the lipid class.

Calculate formula and mass of LPEp

Calculate formula and mass of PC

Calculate formula and mass of LysoPS

Calculate formula and mass of LPAo

annotateIsotopes

Annotate isotopes

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of PIP

Calculate formula and mass of MG

Calculate formula and mass of PI

Calculate formula and mass of PCo

Calculate formula and mass of LysoPCo

Calculate formula and mass of PCp

calculate coelution score between two peaks

Check intensity rules

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of PS

Combine chain fragments that could belong to the same precursor.

MS/MS scan extraction of a precursor in DDA

Creation of a database for TG.

Search of chain specific fragments

Calculate formula and mass of sphingomyelines

Ceramides database

Customizable lipid DBs creator

Cross different candidates tables to remove false positives.

Creation of a database for FAHFA, DG and PL.

Confidence Annotation Levels

Calculate formula and mass of PG

Calculate formula and mass of LPI

Calculate formula and mass of LPG

FAHFAs database

Bile acids conjugates database

Cross the original MS1 peaklist with the annotation results

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

Process mzXML files: peakpicking and deisotoping

Coeluting fragments extraction

EIC extraction based on previous partitions generated by partitioning

Bile acids database

Bile Acids (BA) annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Cholesteryl Esters (CE) annotation for ESI+

findMS2precursor

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

checkIntensityRules

Check intensity rules

Calculate formula and mass of TG

Cardiolipins database

Lysophosphocholines (LPC) annotation for ESI-

Calculate formula and mass of PIP3

Carnitines database

Phosphoinositols (PI) annotation for ESI-

Calculate formula and mass of PIP2

Creation of a database for C.

Lipids annotation for ESI+

Total number of carbons and double bounds

Search for fragments of interest withing a list of coeluting fragments

Diacylglycerols (DG) annotation for ESI+

Cardiolipines (CL) annotation for ESI-

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.

dbSphingolipids

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

mz match withing a vector of mz values

Find candidate precursor from fullMS function

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Ceramides (Cer) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI+

Ceramides (Cer) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI-

getInclusionList

Obtain an inclusion list from the annotation results

Difference between two carbon:bounds structures

Phosphoethanolamines (PE) annotation for ESI-

FAHFA annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Lysophosphoinositols (LPI) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Lysophosphoserines (LPS) annotation for ESI-

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

Sphingoid bases phosphate (SphP) annotation for ESI-

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

Sphingoid bases phosphate (SphP) annotation for ESI+

Monoacylglycerol (MG) annotation for ESI+

Acylcarnitine annotation for ESI+

Phosphocholines (PC) annotation for ESI-

Phosphocholines (PC) annotation for ESI+

Lipids annotation for ESI-

Search of lipid candidates of a certain class

Phosphoserines (PS) annotation for ESI-

Plot informative peaks for lipids annotation

Sphingoid bases (Sph) annotation for ESI-

Sphyngomyelines (SM) annotation for ESI+

Read .mzXML files and initiate msobject

Sphingoid bases (Sph) annotation for ESI-

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

Calculate total number of carbons and double bounds of lipid chains

Sphingoid bases database

organizeResults

Prepare output for LipidMS annotation functions

peak-pick based on previous EIC clusters generated by clustering

Target isotopes search

Sphingoid bases phosphate database

Check matches between chains composition and precursor structures

Lysophosphoethanolamines (LPE) annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Phosphoglycerols (PG) annotation for ESI-

Phosphoglycerols (PG) annotation for ESI+