There are three steps that take time in the work flow: the data conversion from proprietary vendor file format to open mzML or mzXML. This is done under MS Windows with a software called msconvert, without R involvement. Then under R comes the feature detection from the spectroscopic data and the alignment of the features for feature list generation.
At the moment, the converted mzML-files are read in by the R-functions, spectral features are detected and aligned. I would imagine that the "upload" into a Shiny app would take some additional time, is that correct? Ideally, one could also observe and navigate though the data/spectra in a Shiny plot before and after processing, scaling, nomalization etc, which is possible with the R-functions, but requires a lot of knowledge of the workings of these functions.
Sorry my simplistic view and ignorance, but we are at the very first steps of conceptualization and dont have an R-expert at our hands. And before we embark on such a project, we would need to understand the concept and structure.