rawR - Direct access to raw mass spectrometry data in R

The Bioconductor project has shown that the R statistical environment is a highly valuable tool for genomics data analysis [DOI:10.1038/nmeth.3252], but with respect to proteomics we are still missing low level infrastructure to enable performant and robust analysis workflows in R. Fundamentally important are libraries that provide raw data access. Our R package rawDiag [DOI:10.1021/acs.jproteome.8b00173] has provided the proof-of-principle how access to mass spectrometry raw files can be realized by wrapping vendor-provided APIs, but rather focused on meta data analysis and visualization. Our novel package rawR now provides complete, OS independent access to all spectral data logged in Thermo Fisher Scientific raw [URL:https://github.com/fgcz/rawR] files. In this technical note, we present implementation details and describe the main functionality provided by the rawR package. In addition, we report two use cases inspired by real-word research task that demonstrate the application of the package.