rpx

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

Tools for TMT based quantitative proteomics data analysis.

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.