iontree: Data management and analysis of ion trees from ion-trap mass spectrometry

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Ion fragmentation provides structural information for metabolite identification. This package provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Author
Mingshu Cao
Date of publication
None
Maintainer
Mingshu Cao <mingshu.cao@agresearch.co.nz>
License
GPL-2
Version
1.20.0

View on Bioconductor

Man pages

buildIonTree
Build ion tree
createDB
Create a SQLite database
distMS2
Distance metric for MS2 spectral similarity measurement
formatSpec
Format mass spec matrix data into a string format, or vice...
getMetaInfo
Get metadata information from data file in mzXML
getMSnRaw
Get MSn raw data
hasMS2
Check which samples have MS2 spectra generated
iontree-class
Class "iontree"
iontree-package
MSn-iontree: Ion tree management and analysis
metaDataImport
Data entry of meta information
mzImport
Data entry of iontree into mz table
plot-methods
Plot iontree
plotSpectrum
Plot a spectrum
rs2iontree
Convert a data frame into iontree
saveMSnRaw
Retrieve MS2 and MS3 data and save as R binary in the current...
searchMS2
Search MS2 spectrum from sqlite database
show-methods
Show methods for class iontree
topIons
Retain spectrum with the most intense ions

Files in this package

iontree/.BBSoptions
iontree/DESCRIPTION
iontree/LICENSE
iontree/NAMESPACE
iontree/R
iontree/R/AllClasses.R
iontree/R/AllGenerics.R
iontree/R/buildIonTree.R
iontree/R/createDB.R
iontree/R/distMS2.R
iontree/R/formatSpec.R
iontree/R/getMSnRaw.R
iontree/R/getMetaInfo.R
iontree/R/hasMS2.R
iontree/R/metaDataImport.R
iontree/R/mzImport.R
iontree/R/onLoad.R
iontree/R/plotSpectrum.R
iontree/R/rs2iontree.R
iontree/R/saveMSnRaw.R
iontree/R/searchMS2.R
iontree/R/topIons.R
iontree/build
iontree/build/vignette.rds
iontree/inst
iontree/inst/doc
iontree/inst/doc/iontree_doc.R
iontree/inst/doc/iontree_doc.Rnw
iontree/inst/doc/iontree_doc.pdf
iontree/inst/java
iontree/inst/java/jrap_StAX_v5.2.jar
iontree/inst/java/xcms.jar
iontree/inst/sql
iontree/inst/sql/mzDBSchema.sql
iontree/man
iontree/man/buildIonTree.Rd
iontree/man/createDB.Rd
iontree/man/distMS2.Rd
iontree/man/formatSpec.Rd
iontree/man/getMSnRaw.Rd
iontree/man/getMetaInfo.Rd
iontree/man/hasMS2.Rd
iontree/man/iontree-class.Rd
iontree/man/iontree-package.Rd
iontree/man/metaDataImport.Rd
iontree/man/mzImport.Rd
iontree/man/plot-methods.Rd
iontree/man/plotSpectrum.Rd
iontree/man/rs2iontree.Rd
iontree/man/saveMSnRaw.Rd
iontree/man/searchMS2.Rd
iontree/man/show-methods.Rd
iontree/man/topIons.Rd
iontree/vignettes
iontree/vignettes/iontree_doc.Rnw