Lipid Annotation for LC-MS/MS DDA or DIA Data

adductsTable | Adducts table |

annotateIsotopes | Annotate isotopes |

assignDB | Load LipidMS default data bases |

baconjdb | Bile acids conjugates database |

badb | Bile acids database |

carnitinesdb | Carnitines database |

cbs | Total number of carbons and double bounds |

CEdb | CEs database |

cerdb | Ceramides database |

chainFrags | Search of chain specific fragments |

checkClass | Search of class fragments to confirm the lipid class. |

checkIntensityRules | Check intensity rules |

checkIntRules | Check intensity rules |

cldb | Cardiolipins database |

clustering | EIC extraction based on previous partitions generated by... |

coelutingFrags | Coeluting fragments extraction |

coelutionScore | calculate coelution score between two peaks |

combineChains | Combine chain fragments that could belong to the same... |

confLevels | Confidence Annotation Levels |

createLipidDB | Customizable lipid DBs creator |

crossAdducts | Cross different candidates tables to remove false positives. |

crossTables | Cross the original MS1 peaklist with the annotation results |

dataProcessing | Process mzXML files: peakpicking and deisotoping |

dbFourChains | Creation of a database for C. |

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

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

dbThreeChains | Creation of a database for TG. |

dbTwoChains | Creation of a database for FAHFA, DG and PL. |

ddaFrags | MS/MS scan extraction of a precursor in DDA |

dgdb | DGs database |

diffcb | Difference between two carbon:bounds structures |

fadb | FAs database |

fahfadb | FAHFAs database |

filtermsms | Presence or absence of an mz value withing a vector of mz... |

filtrateAdducts | Remove low adduct supported candidates to avoid false... |

findCandidates | Search of lipid candidates of a certain class |

findMS2precursor | find lisnks between MS1 peaks and precursors selected for MS2... |

findPrecursor | Find candidate precursor from fullMS function |

frags | Search for fragments of interest withing a list of coeluting... |

getFormula | Get formula and neutral mass for annotated compounds |

getInclusionList | Obtain an inclusion list from the annotation results |

hfadb | HFAs database |

idBAneg | Bile Acids (BA) annotation for ESI- |

idCarpos | Acylcarnitine annotation for ESI+ |

idCEpos | Cholesteryl Esters (CE) annotation for ESI+ |

idCerneg | Ceramides (Cer) annotation for ESI- |

idCerpos | Ceramides (Cer) annotation for ESI+ |

idCLneg | Cardiolipines (CL) annotation for ESI- |

idDGpos | Diacylglycerols (DG) annotation for ESI+ |

idFAHFAneg | FAHFA annotation for ESI- |

idFAneg | Fatty Acids (FA) annotation for ESI- |

idLPCneg | Lysophosphocholines (LPC) annotation for ESI- |

idLPCpos | Lysophosphocholines (LPC) annotation for ESI+ |

idLPEneg | Lysophosphoethanolamines (LPE) annotation for ESI- |

idLPEpos | Lysophosphoethanolamines (LPE) annotation for ESI+ |

idLPGneg | Lysophosphoglycerols (LPG) annotation for ESI- |

idLPIneg | Lysophosphoinositols (LPI) annotation for ESI- |

idLPSneg | Lysophosphoserines (LPS) annotation for ESI- |

idMGpos | Monoacylglycerol (MG) annotation for ESI+ |

idNEG | Lipids annotation for ESI- |

idPCneg | Phosphocholines (PC) annotation for ESI- |

idPCpos | Phosphocholines (PC) annotation for ESI+ |

idPEneg | Phosphoethanolamines (PE) annotation for ESI- |

idPEpos | Phosphoethanolamines (PE) annotation for ESI+ |

idPGneg | Phosphoglycerols (PG) annotation for ESI- |

idPGpos | Phosphoglycerols (PG) annotation for ESI+ |

idPIneg | Phosphoinositols (PI) annotation for ESI- |

idPOS | Lipids annotation for ESI+ |

idPSneg | Phosphoserines (PS) annotation for ESI- |

idSMpos | Sphyngomyelines (SM) annotation for ESI+ |

idSphneg | Sphingoid bases (Sph) annotation for ESI- |

idSphPneg | Sphingoid bases phosphate (SphP) annotation for ESI- |

idSphpos | Sphingoid bases (Sph) annotation for ESI- |

idSphPpos | Sphingoid bases phosphate (SphP) annotation for ESI+ |

idTGpos | Triacylglycerols (TG) annotation for ESI+ |

joinfrags | Join fragments information when several peaks of the same... |

LipidMSapp | LipidMS shiny app |

lysopadb | LPAs database |

lysopcdb | LPCs database |

lysopedb | LPEs database |

lysopgdb | LPGs database |

lysopidb | LPIs database |

lysopsdb | LPSs database |

MassCarnitines | Calculate formula and mass of carnitines |

MassCE | Calculate formula and mass of cholesterol esthers |

MassCer | Calculate formula and mass of ceramides |

MassCerP | Calculate formula and mass of ceramides phosphate |

MassCL | Calculate formula and mass of CL |

MassDG | Calculate formula and mass of DG |

MassFA | Calculate formula and mass of fatty acids |

MassFAHFA | Calculate formula and mass of FAHFA |

MassGlcCer | Calculate formula and mass of glucoceramides |

MassHFA | Calculate formula and mass of hydroxi fatty acids |

MassLysoPA | Calculate formula and mass of LPA |

MassLysoPAo | Calculate formula and mass of LPAo |

MassLysoPC | Calculate formula and mass of LysoPC |

MassLysoPCo | Calculate formula and mass of LysoPCo |

MassLysoPCp | Calculate formula and mass of LysoPCp |

MassLysoPE | Calculate formula and mass of LPE |

MassLysoPEo | Calculate formula and mass of LPEo |

MassLysoPEp | Calculate formula and mass of LPEp |

MassLysoPG | Calculate formula and mass of LPG |

MassLysoPI | Calculate formula and mass of LPI |

MassLysoPS | Calculate formula and mass of LysoPS |

MassMG | Calculate formula and mass of MG |

MassPA | Calculate formula and mass of PA |

MassPC | Calculate formula and mass of PC |

MassPCo | Calculate formula and mass of PCo |

MassPCp | Calculate formula and mass of PCp |

MassPE | Calculate formula and mass of PE |

MassPEo | Calculate formula and mass of plasmanyl PE |

MassPEp | Calculate formula and mass of plasmenyl PE |

MassPG | Calculate formula and mass of PG |

MassPI | Calculate formula and mass of PI |

MassPIP | Calculate formula and mass of PIP |

MassPIP2 | Calculate formula and mass of PIP2 |

MassPIP3 | Calculate formula and mass of PIP3 |

MassPS | Calculate formula and mass of PS |

MassSM | Calculate formula and mass of sphingomyelines |

MassSph | Calculate formula and mass of sphingoid bases |

MassSphP | Calculate formula and mass of sphingoid phosphate bases |

MassTG | Calculate formula and mass of TG |

mgdb | MGs database |

mzMatch | mz match withing a vector of mz values |

nlsphdb | Neutral losses db for sphingoid bases. It is employed by... |

organizeResults | Prepare output for LipidMS annotation functions |

padb | PAs database |

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

pcdb | PCs database |

peakdetection | peak-pick based on previous EIC clusters generated by... |

pedb | PEs database |

pgdb | PGs database |

pidb | PIs database |

plotLipids | Plot informative peaks for lipids annotation |

psdb | PSs database |

readMSfile | Read .mzXML files and initiate msobject |

searchIsotopes | Target isotopes search |

select | Check matches between chains composition and precursor... |

smdb | SMs database |

sphdb | Sphingoid bases database |

sphPdb | Sphingoid bases phosphate database |

sumChains | Calculate total number of carbons and double bounds of lipid... |

tgdb | TGs database |

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