Workflow to process tandem MS files and build MassBank records

Bioconductor version: Development (3.0)

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Author: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze

Maintainer: RMassBank at Eawag <massbank at eawag.ch>

To install this package, start R and enter:


Citation (from within R, enter citation("RMassBank")):


PDF R Script RMassBank non-standard usage
PDF R Script RMassBank using XCMS walkthrough
PDF R Script RMassBank walkthrough
PDF   Reference Manual


biocViews Bioinformatics, MassSpectrometry, Metabolomics, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends Rcpp
Imports XML, RCurl, rjson, rcdk, yaml, mzR, methods
Suggests gplots, RMassBankData, xcms(>= 1.37.1), CAMERA, ontoCAT, RUnit
System Requirements OpenBabel
Depends On Me
Imports Me
Suggests Me RMassBankData

Package Downloads

Package Source RMassBank_1.7.0.tar.gz
Windows Binary RMassBank_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) RMassBank_1.7.0.tgz
Mac OS X 10.9 (Mavericks) RMassBank_1.7.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center