LC/MS processing and analysis packages


I have been searching for r packages for the processing and analysis of LC/MS data.  I found xcms, MITE and apLCMS.  Can these packages be used indistinctly to any data collection method (HPLC, Reverse HPLC, LC/MS, LC/MS/MS, high resolution LC/MS…), or are there any specifications to much tha pckage to the data collection method?