LipidMS3.0.5 package

Total number of carbons and double bounds

Coeluting fragments extraction

calculate coelution score between two peaks

Combine chain fragments that could belong to the same precursor.

Search for fragments of interest withing a list of coeluting fragments

Extract peaks from all msobjects in a msbatch.

Write features table based on groups

Get formula and neutral mass for annotated compounds

Obtain an inclusion list from the annotation results

mz match withing a vector of mz values

Calculate formula and mass of ceramides

Calculate formula and mass of ceramides phosphate

Calculate formula and mass of CL

Calculate formula and mass of DG

Calculate formula and mass of fatty acids

Calculate formula and mass of FAHFA

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 LPAo

Calculate formula and mass of LysoPC

Calculate formula and mass of LysoPCo

Calculate formula and mass of LysoPCp

Calculate formula and mass of LPE

Calculate formula and mass of LPEo

Calculate formula and mass of LPEp

Calculate formula and mass of LPG

Calculate formula and mass of LPI

Calculate formula and mass of LysoPS

Calculate formula and mass of MG

Calculate formula and mass of PA

Calculate formula and mass of PC

Calculate formula and mass of PCo

Calculate formula and mass of PCp

Calculate formula and mass of PE

Calculate formula and mass of plasmanyl PE

Calculate formula and mass of plasmenyl PE

Calculate formula and mass of PG

Calculate formula and mass of PI

Calculate formula and mass of PIP

Calculate formula and mass of PIP2

Calculate formula and mass of PIP3

Calculate formula and mass of PS

Calculate formula and mass of sphingomyelines

Calculate formula and mass of sphingoid bases

Calculate formula and mass of sphingoid phosphate bases

Calculate formula and mass of TG

EIC extraction based on previous partitions generated by partitioning

Creation of a database for FAHFA, DG and PL.

Sphyngomyelines (SM) annotation for ESI+

Sphingoid bases (Sph) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI-

Sphingoid bases (Sph) annotation for ESI-

Sphingoid bases phosphate (SphP) annotation for ESI+

Triacylglycerols (TG) annotation for ESI+

Index partitions or clusters assigned during alignment.

Calculate max distance between clusters.

Summarize annotation results from an msbatch into the features table

Join fragments information when several peaks of the same fragment are...

LipidMS shiny app

Align samples from an msbatch

Annotate isotopes

Lipid annotation for an msbatch

Load LipidMS default data bases

Process several mzXML files (peakpicking and isotope annotation) and c...

Calculate formula and mass of acylceramides

Search of chain specific fragments

extract chains composition from a lipid name

Search of class fragments to confirm the lipid class.

Check intensity rules

Check intensity rules

Clustering for MS peaks based on mz or RT.

Customizable lipid DBs creator

Cross different candidates tables to remove false positives.

Cross the original MS1 peaklist with the annotation results

Process mzXML files individually: peakpicking and isotope annotation

Creation of a database for C.

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

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

Creation of a database for TG.

MS/MS scan extraction of a precursor in DDA

Difference between two carbon:bounds structures

Fill peaks from a grouped msbatch

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

Remove low adduct supported candidates to avoid false positives.

Search of lipid candidates of a certain class

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

Find candidate precursor from fullMS function

Group features from an msbatch

Acylceramides (AcylCer) annotation for ESI-

Acylceramides (AcylCer) annotation for ESI+

Bile Acids (BA) annotation for ESI-

Acylcarnitine annotation for ESI+

Cholesteryl Esters (CE) annotation for ESI+

Ceramides (Cer) annotation for ESI-

Ceramides phosphate (CerP) annotation for ESI-

Ceramides (Cer) annotation for ESI+

Ceramides phosphate (CerP) annotation for ESI+

Cardiolipines (CL) annotation for ESI-

Diacylglycerols (DG) annotation for ESI+

FAHFA annotation for ESI-

Fatty Acids (FA) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI-

Lysophosphocholines (LPC) annotation for ESI+

Lysophosphoethanolamines (LPE) annotation for ESI-

Lysophosphoethanolamines (LPE) annotation for ESI+

Lysophosphoglycerols (LPG) annotation for ESI-

Lysophosphoinositols (LPI) annotation for ESI-

Lysophosphoserines (LPS) annotation for ESI-

Monoacylglycerol (MG) annotation for ESI+

Calculate formula and mass of carnitines

Calculate formula and mass of cholesterol esthers

Lipids annotation for ESI-

Phosphocholines (PC) annotation for ESI-

Plasmanyl Phosphocholines (PCo) annotation for ESI-

Plasmanyl Phosphocholines (PCo) annotation for ESI+

Plasmenyl Phosphocholines (PCp) annotation for ESI-

Phosphocholines (PC) annotation for ESI+

Plasmenyl Phosphocholines (PCp) annotation for ESI+

Phosphoethanolamines (PE) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-

Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-

Phosphoethanolamines (PE) annotation for ESI+

Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+

Phosphoglycerols (PG) annotation for ESI-

Phosphoglycerols (PG) annotation for ESI+

Phosphoinositols (PI) annotation for ESI-

Phosphoinositols (PI) annotation for ESI+

Lipids annotation for ESI+

Phosphoserines (PS) annotation for ESI-

Sphingomyelines (SM) annotation for ESI-

Prepare output for LipidMS annotation functions

agglomarative partitioning for LC-HRMS data based on enviPick algorith...

peak-pick based on previous EIC clusters generated by clustering

EIC for all samples in a msbatch

Plot informative peaks for lipid annotation

TIC for all samples in a msbatch

Read mzXML file and initiate msobject

Correct RT based on a rtmodel.

Plot retention time deviation

Targeted isotopes search

Targeted isotopes search for msbatch

Check matches between chains composition and precursor structures

Create msbatch for batch processing.

Calculate total number of carbons and double bounds of lipid chains