It would be useful to have a bit more information regarding the type of label-free and what kind of analysis you are after. In terms of statistical analysis, standard packages can be applied to proteomics data, but you might also want to have a look at MSstats in particular. In terms of MS data processing, for MS2 label-free (peptide/spectral counting), you could look at MSnID, msmsTests and MSnbase. For MS1 quantitation, I think the best solution would be to try xcms that is usually used for metabolomics data. You could also use a third party software and then import the data into R as MSnSet instances using readMSnSet or readMSnSet2 from MSnbase, that will manage the quantitative data and meta-date and provide support for various analyses.
As a general introduction to R/Bioc for proteomics, you could look at the RforProteomics package vignette.