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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.
Gatto et al. (Wed,) studied this question.