This vignette describes MSnbase’s input and output capabilities.
MSnbase 2.2.0
MSnbase is under active development; current functionality is evolving and new features will be added. This software is free and open-source software. If you use it, please support the project by citing it in publications:
Laurent Gatto and Kathryn S. Lilley. MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics 28, 288-289 (2011).
For bugs, typos, suggestions or other questions, please file an issue in our tracking system (https://github.com/lgatto/MSnbase/issues) providing as much information as possible, a reproducible example and the output of sessionInfo().
If you don’t have a GitHub account or wish to reach a broader audience for general questions about proteomics analysis using R, you may want to use the Bioconductor support site: https://support.bioconductor.org/.
MSnbase’s aims are to facilitate the reproducible analysis of mass spectrometry data within the R environment, from raw data import and processing, feature quantification, quantification and statistical analysis of the results (Gatto and Lilley 2012). Data import functions for several formats are provided and intermediate or final results can also be saved or exported. These capabilities are presented below.
Data stored in one of the published XML-based formats. i.e. mzXML (Pedrioli et al. 2004), mzData (Orchard et al. 2007) or mzML (Martens et al. 2010), can be imported with the readMSData method, which makes use of the mzR package to create MSnExp objects. The files can be in profile or centroided mode. See ?readMSData for details.
Peak lists in the mgf format1 http://www.matrixscience.com/help/data_file_help.html can be imported using the readMgfData. In this case, the peak data has generally been pre-processed by other software. See ?readMgfData for details.
Third party software can be used to generate quantitative data and exported as a spreadsheet (generally comma or tab separated format). This data as well as any additional meta-data can be imported with the readMSnSet function. See ?readMSnSet for details.
MSnbase also supports the mzTab format2 https://github.com/HUPO-PSI/mzTab, a light-weight, tab-delimited file format for proteomics data developed within the Proteomics Standards Initiative (PSI). mzTab files can be read into R with readMzTabData to create and MSnSet instance.