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LipidMS

LipidMS R package (v.2.1)

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Version

Install

install.packages('LipidMS')

Monthly Downloads

282

Version

2.1.2

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

March 2nd, 2021

Functions in LipidMS (2.1.2)

Calculate formula and mass of fatty acids

Calculate formula and mass of hydroxi fatty acids

Calculate formula and mass of glucoceramides

Calculate formula and mass of PE

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of ceramides

Calculate formula and mass of sphingoid bases

Calculate formula and mass of LPA

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of PCo

Calculate formula and mass of LPAo

Calculate formula and mass of PA

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of PCp

Calculate formula and mass of PC

Calculate formula and mass of PIP2

calculate coelution score between two peaks

Calculate formula and mass of PIP3

Calculate formula and mass of LPE

Calculate formula and mass of PS

Calculate formula and mass of LysoPCp

Calculate formula and mass of LysoPS

Calculate formula and mass of cholesterol esthers

Calculate formula and mass of DG

Calculate formula and mass of CL

Calculate formula and mass of sphingomyelines

Calculate formula and mass of LysoPC

Cross different candidates tables to remove false positives.

Combine chain fragments that could belong to the same precursor.

Cross the original MS1 peaklist with the annotation results

filtrateAdducts

Remove low adduct supported candidates to avoid false positives.

Calculate formula and mass of PI

checkIntensityRules

Check intensity rules

Load LipidMS default data bases

Calculate formula and mass of PIP

Calculate formula and mass of MG

Calculate formula and mass of TG

annotateIsotopes

Annotate isotopes

Cardiolipins database

Search of lipid candidates of a certain class

MS/MS scan extraction of a precursor in DDA

Calculate formula and mass of LysoPCo

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

Search of chain specific fragments

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of PG

Bile acids conjugates database

Calculate formula and mass of LPI

Ceramides database

Calculate formula and mass of LPG

LipidMS shiny app

Bile acids database

EIC extraction based on previous partitions generated by partitioning

Search of class fragments to confirm the lipid class.

Creation of a database for TG.

getInclusionList

Obtain an inclusion list from the annotation results

Coeluting fragments extraction

Cardiolipines (CL) annotation for ESI-

Creation of a database for FAHFA, DG and PL.

Acylcarnitine annotation for ESI+

Check intensity rules

Find candidate precursor from fullMS function

findMS2precursor

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

Sphingoid bases (Sph) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Phosphoinositols (PI) annotation for ESI-

FAHFAs database

Calculate formula and mass of LPEo

Lipids annotation for ESI+

Carnitines database

Total number of carbons and double bounds

Calculate formula and mass of LPEp

Diacylglycerols (DG) annotation for ESI+

Customizable lipid DBs creator

Creation of a database for C.

Search for fragments of interest withing a list of coeluting fragments

Confidence Annotation Levels

Process mzXML files: peakpicking and deisotoping

Bile Acids (BA) annotation for ESI-

Cholesteryl Esters (CE) annotation for ESI+

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

Difference between two carbon:bounds structures

Sphingoid bases (Sph) annotation for ESI-

Get formula and neutral mass for annotated compounds

Lipids annotation for ESI-

Monoacylglycerol (MG) annotation for ESI+

FAHFA annotation for ESI-

Target isotopes search

mz match withing a vector of mz values

Check matches between chains composition and precursor structures

Phosphoserines (PS) annotation for ESI-

Sphyngomyelines (SM) annotation for ESI+

Lysophosphoinositols (LPI) annotation for ESI-

Lysophosphoglycerols (LPG) annotation for ESI-

Phosphoglycerols (PG) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI-

peak-pick based on previous EIC clusters generated by clustering

Sphingoid bases phosphate (SphP) annotation for ESI+

Lysophosphoserines (LPS) annotation for ESI-

Triacylglycerols (TG) annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Lysophosphocholines (LPC) annotation for ESI+

Ceramides (Cer) annotation for ESI+

Ceramides (Cer) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI-

Phosphocholines (PC) annotation for ESI+

Phosphocholines (PC) annotation for ESI-

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

agglomarative partitioning for LC-HRMS data based on enviPick algorithm

Plot informative peaks for lipids annotation

organizeResults

Prepare output for LipidMS annotation functions

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

Read .mzXML files and initiate msobject

Sphingoid bases phosphate database

Sphingoid bases database

Calculate total number of carbons and double bounds of lipid chains

Calculate formula and mass of carnitines

Calculate formula and mass of FAHFA