Package: MetaboAnnotatoR 1.1.1

Goncalo Graca

MetaboAnnotatoR: Automated Annotation of All-Ion Fragmentation LC-MS Metabolomic Features

Performs feature annotations on LC-MS All-ion fragmentation datasets using fragment ion libraries.

Authors:Goncalo Graca [aut, cre], Yuheng Cai [aut], Timothy Ebbels [aut]

MetaboAnnotatoR_1.1.1.tar.gz
MetaboAnnotatoR_1.1.1.zip(r-4.7)MetaboAnnotatoR_1.1.1.zip(r-4.6)MetaboAnnotatoR_1.1.1.zip(r-4.5)
MetaboAnnotatoR_1.1.1.tgz(r-4.6-any)MetaboAnnotatoR_1.1.1.tgz(r-4.5-any)
MetaboAnnotatoR_1.1.1.tar.gz(r-4.7-any)MetaboAnnotatoR_1.1.1.tar.gz(r-4.6-any)
MetaboAnnotatoR_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetaboAnnotatoR/json (API)
NEWS

# Install 'MetaboAnnotatoR' in R:
install.packages('MetaboAnnotatoR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gggraca/metaboannotator/issues

Datasets:
  • acetaminophen - MetaboAnnotatoR fragment database entry for Acetaminophen Positive mode
  • LipidNeg - MetaboAnnotatoR Lipid Negative fragment libraries
  • LipidPos - MetaboAnnotatoR Lipid Positive fragment libraries
  • MetabolitesNeg - MetaboAnnotatoR Metabolite Negative fragment libraries
  • MetabolitesPos - MetaboAnnotatoR Metabolite Positive fragment libraries
  • pseudoMSMS - MetaboAnnotatoR-generated example pseudoMSMS spectrum and related data
  • RC - Pseudo-MS/MS spectra from MESA Lipid Positive LC-MS serum samples
  • rCandidates - MetaboAnnotatoR-generated example of ranked annotation candidates
  • xset - MESA cohort subset Lipid Positive LC-MS samples processed using XCMS

On BioConductor:MetaboAnnotatoR-1.1.0(bioc 3.24)MetaboAnnotatoR-1.0.0(bioc 3.23)

massspectrometrymetabolomics

6.55 score 14 stars 4 scripts 162 downloads 14 exports 136 dependencies

Last updated from:cbb249664f. Checks:1 NOTE, 4 OK, 5 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE228
linux-devel-x86_64OK581
source / vignettesOK363
linux-release-x86_64OK540
macos-release-arm64WARNING484
macos-oldrel-arm64WARNING313
windows-develWARNING583
windows-releaseWARNING577
windows-oldrelWARNING566
wasm-releaseOK159

Exports:annotateAIFannotateISFannotateRCcheckIsotopecompFraggenFragEntrygetPseudoMSMSmspToLibplotResultSpecrankScoreRCspecsaveAnnotationssearchLibxcmsSpec

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

Generate metabolite library entries

Gonçalo Graça

Rendered fromgen_library_entry.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-03-18
Started: 2021-07-24

Import an MS/MS library

Gonçalo Graça

Rendered fromimport_from_msp.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-03-10
Started: 2021-11-28

Introduction to MetaboAnnotatoR

Gonçalo Graça

Rendered fromMetaboAnnotatoR.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-03-18
Started: 2026-01-22

Readme and manuals

Help Manual

Help pageTopics
MetaboAnnotatoR fragment database entry for Acetaminophen Positive modeacetaminophen
Annotate features from LC-MS AIF raw chromatogramsannotateAIF
Annotate features from LC-MS (MS1 only) raw chromatogramsannotateISF
Annotate features from LC-MS AIF datasets processed with RAMClustRannotateRC
Isotopologue type determinationcheckIsotope
Match (pseudo-)MS/MS spectra ions to library fragmentscompFrag
Generate a fragment library entrygenFragEntry
Obtain pseudo-MS/MS spectra for an LC-MS feature of interestgetPseudoMSMS
MetaboAnnotatoR Lipid Negative fragment librariesLipidNeg
MetaboAnnotatoR Lipid Positive fragment librariesLipidPos
MetaboAnnotatoR Metabolite Negative fragment librariesMetabolitesNeg
MetaboAnnotatoR Metabolite Positive fragment librariesMetabolitesPos
Generate metabolite entries from MS/MS spectra (.msp files)mspToLib
Plot pseudo-MS/MS composed of candidate matched ionsplotResultSpec
MetaboAnnotatoR-generated example pseudoMSMS spectrum and related datapseudoMSMS
Rank candidate metabolite annotations by scorerankScore
Pseudo-MS/MS spectra from MESA Lipid Positive LC-MS serum samplesRC
MetaboAnnotatoR-generated example of ranked annotation candidatesrCandidates
Get RAMClustR pseudo-MS/MS spectra (cluster).RCspec
Save annotation resultssaveAnnotations
Search candidate metabolites from the fragments librariessearchLib
Extract the low- and high-collision-energy spectra from XCMS object (from AIF data)xcmsSpec
MESA cohort subset Lipid Positive LC-MS samples processed using XCMSxset