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LipidMS (version 1.2.0)

Lipid Annotation for LC-MS/MS DIA Data

Description

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

1.2.0

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

November 20th, 2020

Functions in LipidMS (1.2.0)

Calculate formula and mass of fatty acids

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of CL

Calculate formula and mass of carnitines

Calculate formula and mass of ceramides

Calculate formula and mass of DG

Calculate formula and mass of FAHFA

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of LPEp

Calculate formula and mass of glucoceramides

Calculate formula and mass of LPE

Calculate formula and mass of LPA

Calculate formula and mass of LPG

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of PCp

Calculate formula and mass of sphingomyelines

load LipidMS default data bases

Calculate formula and mass of sphingoid bases

Calculate formula and mass of PE

Calculate formula and mass of LPEo

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of LPAo

Calculate formula and mass of MG

Calculate formula and mass of LysoPCo

Calculate formula and mass of LysoPCp

Calculate formula and mass of LysoPS

Calculate formula and mass of PIP3

Calculate formula and mass of LPI

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of PS

calculate coelution score between two peaks

Combine chain fragments that could belong to the same precursor.

Bile acids conjugates database

Coeluting fragments extraction

Calculate formula and mass of PA

Cardiolipins database

Lysophosphocholines (LPC) annotation for ESI+

Calculate formula and mass of sphingoid phosphate bases

Creation of a database for TG.

Creation of a database for FAHFA, DG and PL.

Calculate formula and mass of PC

Calculate formula and mass of LysoPC

FAHFAs database

Search of chain specific fragments

Calculate formula and mass of PI

Calculate formula and mass of PCo

Calculate formula and mass of PG

Calculate formula and mass of TG

Total number of carbons and double bounds

Lysophosphoserines (LPS) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI-

Search of class fragments to confirm the lipid class.

checkIntensityRules

Check intensity rules

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

Check intensity rules

annotateIsotopes

Annotate isotopes

ceramides database

Cross different candidates tables to remove false positives.

getInclusionList

Obtain an inclusion list from the annotation results

Cross the original MS1 peaklist with the annotation results

Calculate formula and mass of PIP

dbSphingolipids

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

Search of lipid candidates of a certain class.

Find candidate precursor from fullMS function

Target isotopes search

Sphingoid bases database

Calculate total number of carbons and double bounds of lipid chains

Calculate formula and mass of PIP2

Difference between two carbon:bounds structures

Phosphoethanolamines (PE) annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI-

Phosphoglycerols (PG) annotation for ESI-

Process mzXML files: peakpicking and deisotoping

Bile acids database

Carnitines database

Phosphoinositols (PI) annotation for ESI-

Customizable lipid DBs creator

Confidence Annotation Levels

Diacylglycerols (DG) annotation for ESI+

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

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

Lysophosphoethanolamines (LPE) annotation for ESI+

FAHFA annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Monoacylglycerol (MG) annotation for ESI+

Lipids annotation for ESI-

Lysophosphoglycerols (LPG) annotation for ESI-

Phosphoserines (PS) annotation for ESI-

Lipids annotation for ESI+

Sphingoid bases phosphate (SphP) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Cholesterol Esthers (CE) annotation for ESI+

Bile Acids (BA) annotation for ESI-

mz match withing a vector of mz values

Ceramides (Cer) annotation for ESI-

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

Ceramides (Cer) annotation for ESI+

Sphyngomyelines (SM) annotation for ESI+

Sphingoid bases phosphate (SphP) annotation for ESI-

Creation of a database for C.

Search for fragments of interest withing a list of coeluting fragments

Cardiolipines (CL) annotation for ESI-

Carnitine annotation for ESI+

Get formula and neutral mass for annotated compounds

Phosphocholines (PC) annotation for ESI-

Phosphocholines (PC) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Check matches between chains composition and precursor structures

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

Separate .mzXML files by CE

Sphingoid bases phosphate database

organizeResults

Prepare output for LipidMS annotation functions