Abstract
We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing, and visualization of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualization.
Highlights
Mass spectrometry is a powerful technology to assay chemical and biological samples
The complexity and size of these data constitute a signicant challenge for protocol development: in addition to the development of sample processing and mass spectrometry methods that yield the raw data, it is essential to process, analyse, interpret and assess these new data to demonstrate the improvement in the technical, analytical and computational workows
These range from low level software libraries that are aimed at programmers to enable the development of new applications, to more user-oriented applications with graphical user interfaces which provide a more limited set of functionalities to address a dened scope
Summary
Mass spectrometry is a powerful technology to assay chemical and biological samples. It is used in routine applications with well characterised protocols such as in clinical settings, as well as a development platform, with the aim to improve on existing protocols and devise new ones. MSnbase relies on the mzR package[2] to import raw mass spectrometry data from one of the many community-maintained open standards formats (mzML, mzXML, mzData or ANDI-MS/netCDF) and provides a rich and principled interface to manipulate such objects. The on-disk backend only loads the metadata into memory when the on-disk MSnExp is created and accesses the spectra data (i.e. m/z and intensity values) in the original les on disk only when needed (see below and Figure 2 (d)), such as for example for plotting. All the functions for the processing of BoxCar spectra and segments in MSnbaseBoxCar were developed using existing functionality implemented in MSnbase, illustrating the exibility and adaptability of the MSnbase package for computational mass spectrometry method development. The growth of MSnbase and the user support provided over the years attest to the core maintainers commitment to long-term development, and the quality and maintainability of the code base
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