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LipidMS (version 1.0.0)

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.

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Version

Install

install.packages('LipidMS')

Monthly Downloads

327

Version

1.0.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

October 15th, 2018

Functions in LipidMS (1.0.0)

Example MS1 data set for id functions in ESI+

Calculate formula and mass of LPI

Calculate formula and mass of LysoPC

Calculate formula and mass of LPE

Calculate formula and mass of TG

Calculate formula and mass of LysoPS

Calculate formula and mass of MG

Example MS2 data set for id functions in ESI+ (high energy)

Total number of carbons and double bounds

Check intensity rules

Calculate formula and mass of CL

Calculate formula and mass of carnitines

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of LPA

Calculate formula and mass of PA

checkIntensityRules

Check intensity rules

Calculate formula and mass of cholesterol esthers

Cross the original MS1 peaklist with the annotation results

Cross different candidates tables to remove false positives.

ceramides database

calculate coelution score between two peaks

Coeluting fragments extraction

Combine chain fragments that could belong to the same precursor.

Calculate formula and mass of PC

Cardiolipins database

Calculate formula and mass of PIP3

Calculate formula and mass of PIP2

FAHFAs database

Ceramides (Cer) annotation for ESI+

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

Lysophosphoethanolamines (LPE) annotation for ESI-

Bile Acids (BA) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

Phosphoserines (PS) annotation for ESI-

Calculate formula and mass of ceramides

Search of lipid candidates of a certain class.

FAHFA annotation for ESI-

Sphyngomyelines (SM) annotation for ESI+

Fatty Acids (FA) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of PS

Diacylglycerols (DG) annotation for ESI+

Calculate formula and mass of sphingomyelines

Lysophosphoserines (LPS) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

Monoacylglycerol (MG) annotation for ESI+

Example MS1 data set for id functions in ESI-

Phosphocholines (PC) annotation for ESI+

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

Search of chain specific fragments

Phosphoethanolamines (PE) annotation for ESI-

Calculate formula and mass of FAHFA

Calculate formula and mass of glucoceramides

mz match withing a vector of mz values

Search of class fragments to confirm the lipid class.

Calculate formula and mass of PE

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

Calculate formula and mass of PG

load LipidMS default data bases

Bile acids conjugates database

Target isotopes search

Sphingoid bases phosphate database

Bile acids database

Example MS2 data set for id functions in ESI+ (low energy)

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

dbSphingolipids

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

Example MS2 data set for id functions in ESI- (high energy)

Carnitines database

Creation of a database for C.

Process mzXML files: peakpicking and deisotoping

Calculate formula and mass of DG

Calculate formula and mass of fatty acids

Calculate formula and mass of PI

Calculate formula and mass of PIP

Difference between two carbon:bounds structures

Creation of a database for TG.

Creation of a database for FAHFA, DG and PL.

Get formula and neutral mass for annotated compounds

getInclusionList

Obtain an inclusion list from the annotation results

Carnitine annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Ceramides (Cer) annotation for ESI-

Lipids annotation for ESI-

Phosphocholines (PC) annotation for ESI-

Calculate formula and mass of sphingoid bases

Calculate formula and mass of sphingoid phosphate bases

Confidence Annotation Levels

Phosphoinositols (PI) annotation for ESI-

Lipids annotation for ESI+

Customizable lipid DBs creator

Convert peaklist from envipick to a xcmxSet to remove isotopes

Check matches between chains composition and precursor structures

Sphingoid bases database

Separate .mzXML files by CE

Find candidate precursor from fullMS function

Search for fragments of interest withing a list of coeluting fragments

Calculate total number of carbons and double bounds of lipid chains

Cholesterol Esthers (CE) annotation for ESI+

Cardiolipines (CL) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Sphingoid bases (Sph) annotation for ESI-

Sphingoid bases (Sph) annotation for ESI-

organizeResults

Prepare output for LipidMS annotation functions

Example MS2 data set for id functions in ESI- (low energy)

Calculate formula and mass of LPG