I have not read the paper you reference, so I can't comment on reproducing exactly what they have done. But if you want to get started with PRIDE data in R, you could get a go with the rpx Bioconductor package that will allow you to query the files for a given ProteomeXchange project (in your case PXD000047). The authors have used Proteome Discoverer (PD), a commercial software. There are ways to process the data in R and/or other alternatives. If you have access to PD, you will be able to import that data into R with MSbase's readMSnSet2 function, which should get you started to use MSstats. The authors have also deposited the mzTab files (processed quantitation data), which you should be able to import into R with MSnbase::readMzTabData (please get in touch if you have issues with the latter).