# LipidMS v0.1.0

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## Lipid Annotation for LC-MS/MS using Data Independent Acquisition

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

## Functions in LipidMS

Name | Description | |

MassGlcCer | Calculate formula and mass of glucoceramides | |

MassPI | Calculate formula and mass of PI | |

idCLneg | Cardiolipines (CL) annotation for ESI- | |

idCarpos | Carnitine annotation for ESI+ | |

idPCneg | Phosphocholines (PC) annotation for ESI- | |

idLPEneg | Lysophosphoethanolamines (LPE) annotation for ESI- | |

idLPCpos | Lysophosphocholines (LPC) annotation for ESI+ | |

idTGpos | Triacylglycerols (TG) annotation for ESI+ | |

MassHFA | Calculate formula and mass of hydroxi fatty acids | |

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

organizeResults | Prepare output for LipidMS annotation functions | |

idPCpos | Phosphocholines (PC) annotation for ESI+ | |

mix_pos_Ce20 | Peak list example of MSMS1 obtained from a mix of standards. | |

mix_neg_fullMS | Peak list example of MS1 obtained from a mix of standards. | |

padb | PAs database | |

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

CEdb | CEs database | |

MassLysoPS | Calculate formula and mass of LysoPS | |

MassSph | Calculate formula and mass of sphingoid bases | |

MassMG | Calculate formula and mass of MG | |

MassCE | Calculate formula and mass of cholesterol esthers | |

baconjdb | Bile acids conjugates database | |

tgdb | TGs database | |

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

MassLysoPG | Calculate formula and mass of LPG | |

MassFAHFA | Calculate formula and mass of FAHFA | |

createLipidDB | Customizable lipid DBs creator | |

confLevels | Confidence Annotation Levels | |

MassSM | Calculate formula and mass of sphingomyelines | |

diffcb | Difference between two carbon:bounds structures | |

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

checkIntRules | Check intensity rules | |

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

dbFourChains | Creation of a database for C. | |

MassSphP | Calculate formula and mass of sphingoid phosphate bases | |

badb | Bile acids database | |

MassLysoPI | Calculate formula and mass of LPI | |

dgdb | DGs database | |

MassLysoPA | Calculate formula and mass of LPA | |

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

getFormula | Get formula and neutral mass for annotated compounds | |

MassTG | Calculate formula and mass of TG | |

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

fadb | FAs database | |

idCerneg | Ceramides (Cer) annotation for ESI- | |

adductsTable | Adducts table | |

checkIntensityRules | Check intensity rules | |

idLPEpos | Lysophosphoethanolamines (LPE) annotation for ESI+ | |

idCerpos | Ceramides (Cer) annotation for ESI+ | |

MassPE | Calculate formula and mass of PE | |

MassPG | Calculate formula and mass of PG | |

cldb | Cardiolipins database | |

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

idLPCneg | Lysophosphocholines (LPC) annotation for ESI- | |

idLPGneg | Lysophosphoglycerols (LPG) annotation for ESI- | |

idSMpos | Sphyngomyelines (SM) annotation for ESI+ | |

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

coelutingFrags | Coeluting fragments extraction | |

cbs | Total number of carbons and double bounds | |

dataProcessing | Process mzXML files: peakpicking and deisotoping | |

dbThreeChains | Creation of a database for TG. | |

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

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

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

findCandidates | Search of lipid candidates of a certain class. | |

findPrecursor | Find candidate precursor from fullMS function | |

idPGneg | Phosphoglycerols (PG) annotation for ESI- | |

lysopedb | LPEs database | |

getInclusionList | Obtain an inclusion list from the annotation results | |

hfadb | HFAs database | |

idPIneg | Phosphoinositols (PI) annotation for ESI- | |

serum_neg_Ce40 | Peak list example of MSMS2 obtained from a pool of serum samples. | |

lysopgdb | LPGs database | |

serum_neg_fullMS | Peak list example of MS1 obtained from a pool of serum samples. | |

idDGpos | Diacylglycerols (DG) annotation for ESI+ | |

sphPdb | Sphingoid bases phosphate database | |

lysopadb | LPAs database | |

idCEpos | Cholesterol Esthers (CE) annotation for ESI+ | |

fahfadb | FAHFAs database | |

idFAHFAneg | FAHFA annotation for ESI- | |

idPOS | Lipids annotation for ESI+ | |

lysopcdb | LPCs database | |

sphdb | Sphingoid bases database | |

idPSneg | Phosphoserines (PS) annotation for ESI- | |

idLPIneg | Lysophosphoinositols (LPI) annotation for ESI- | |

joinAdducts | Join information about precursor candidates found using different adducts | |

idLPSneg | Lysophosphoserines (LPS) annotation for ESI- | |

idMGpos | Monoacylglycerol (MG) annotation for ESI+ | |

idNEG | Lipids annotation for ESI- | |

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

idPEneg | Phosphoethanolamines (PE) annotation for ESI- | |

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

pedb | PEs database | |

pcdb | PCs database | |

makexcmsSet | Convert peaklist from envipick to a xcmxSet to remove isotopes | |

lysopidb | LPIs database | |

mgdb | MGs database | |

sepByCE | Separate .mzXML files by CE | |

idPEpos | Phosphoethanolamines (PE) annotation for ESI+ | |

lysopsdb | LPSs database | |

pgdb | PGs database | |

mzMatch | mz match withing a vector of mz values | |

serum_neg_Ce20 | Peak list example of MSMS1 obtained from a pool of serum samples. | |

serum_pos_fullMS | Peak list example of MS1 obtained from a pool of serum samples. | |

pidb | PIs database | |

smdb | SMs database | |

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

serum_pos_Ce20 | Peak list example of MSMS1 obtained from a pool of serum samples. | |

removeDGs | remove fragments whose relative intensity to the precursor is less than 10 times smaller | |

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

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

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

mix_neg_Ce20 | Peak list example of MSMS1 obtained from a mix of standards. | |

serum_pos_Ce40 | Peak list example of MSMS2 obtained from a pool of serum samples. | |

mix_neg_Ce40 | Peak list example of MSMS2 obtained from a mix of standards. | |

mix_pos_Ce40 | Peak list example of MSMS2 obtained from a mix of standards. | |

psdb | PSs database | |

mix_pos_fullMS | Peak list example of MS1 obtained from a mix of standards. | |

removeAdducts | remove wrong assigned adducts | |

MassCerP | Calculate formula and mass of ceramides phosphate | |

MassCL | Calculate formula and mass of CL | |

MassCer | Calculate formula and mass of ceramides | |

MassPA | Calculate formula and mass of PA | |

MassPC | Calculate formula and mass of PC | |

cerdb | ceramides database | |

chainFrags | Search of chain specific fragments | |

MassCarnitines | Calculate formula and mass of carnitines | |

MassDG | Calculate formula and mass of DG | |

MassFA | Calculate formula and mass of fatty acids | |

MassPIP2 | Calculate formula and mass of PIP2 | |

carnitinesdb | Carnitines database | |

MassPIP3 | Calculate formula and mass of PIP3 | |

MassLysoPE | Calculate formula and mass of LPE | |

MassLysoPC | Calculate formula and mass of LysoPC | |

MassPS | Calculate formula and mass of PS | |

MassPIP | Calculate formula and mass of PIP | |

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## Details

Type | Package |

License | GPL (>= 2) |

LazyData | TRUE |

RoxygenNote | 6.0.1 |

NeedsCompilation | no |

Packaged | 2018-07-10 11:59:40 UTC; 73581298C |

Repository | CRAN |

Date/Publication | 2018-07-12 10:40:03 UTC |

depends | CAMERA , enviPick , methods , R (>= 2.10) |

Contributors | M Alcoriza-Balaguer, J Garcia-Canaveras |

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