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LipidMS (version 1.1.0)

Lipid Annotation for LC-MS/MS DIA Data

Description

Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity 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

388

Version

1.1.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

October 21st, 2019

Functions in LipidMS (1.1.0)

Calculate formula and mass of LysoPC

Calculate formula and mass of glucoceramides

Creation of a database for FAHFA, DG and PL.

Search of chain specific fragments

Calculate formula and mass of MG

Calculate formula and mass of PG

ceramides database

Calculate formula and mass of LysoPS

Calculate formula and mass of PE

Calculate formula and mass of LPG

checkIntensityRules

Check intensity rules

Calculate formula and mass of PIP2

Calculate formula and mass of LPI

Calculate formula and mass of LPE

Calculate formula and mass of PIP

load LipidMS default data bases

annotateIsotopes

Annotate isotopes

Coeluting fragments extraction

Calculate formula and mass of PI

Calculate formula and mass of PIP3

Calculate formula and mass of hydroxi fatty acids

calculate coelution score between two peaks

Carnitines database

Total number of carbons and double bounds

getInclusionList

Obtain an inclusion list from the annotation results

Cardiolipins database

Fatty Acids (FA) annotation for ESI-

FAHFA annotation for ESI-

Get formula and neutral mass for annotated compounds

Calculate formula and mass of PA

Calculate formula and mass of PC

Calculate formula and mass of LPA

Creation of a database for C.

Combine chain fragments that could belong to the same precursor.

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of sphingoid bases

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

Calculate formula and mass of sphingomyelines

Calculate formula and mass of PS

Find candidate precursor from fullMS function

Confidence Annotation Levels

Search for fragments of interest withing a list of coeluting fragments

Bile acids conjugates database

Calculate formula and mass of TG

Monoacylglycerol (MG) annotation for ESI+

Lysophosphoserines (LPS) annotation for ESI-

Customizable lipid DBs creator

Sphingoid bases (Sph) annotation for ESI-

Cross different candidates tables to remove false positives.

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Difference between two carbon:bounds structures

Search of lipid candidates of a certain class.

Sphingoid bases (Sph) annotation for ESI-

Ceramides (Cer) annotation for ESI+

Diacylglycerols (DG) annotation for ESI+

Phosphocholines (PC) annotation for ESI+

dbSphingolipids

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

FAHFAs database

Lysophosphocholines (LPC) annotation for ESI+

Lipids annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Creation of a database for TG.

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

Phosphocholines (PC) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI-

Carnitine annotation for ESI+

mz match withing a vector of mz values

Search of class fragments to confirm the lipid class.

Cross the original MS1 peaklist with the annotation results

Bile acids database

Check intensity rules

Ceramides (Cer) annotation for ESI-

Process mzXML files: peakpicking and deisotoping

Sphingoid bases phosphate (SphP) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Phosphoserines (PS) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Sphyngomyelines (SM) annotation for ESI+

Bile Acids (BA) annotation for ESI-

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

Cholesterol Esthers (CE) annotation for ESI+

Cardiolipines (CL) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

Phosphoinositols (PI) annotation for ESI-

Lipids annotation for ESI+

Target isotopes search

Calculate total number of carbons and double bounds of lipid chains

Check matches between chains composition and precursor structures

organizeResults

Prepare output for LipidMS annotation functions

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

Phosphoethanolamines (PE) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Separate .mzXML files by CE

Sphingoid bases phosphate database

Sphingoid bases database

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of carnitines

Calculate formula and mass of ceramides

Calculate formula and mass of CL

Calculate formula and mass of FAHFA

Calculate formula and mass of DG

Calculate formula and mass of fatty acids