Our differential expression (DE) workflow uses the limma method and R package (initially designed for microarrays).
limma performs DE using linear models, therefore parametric tests. While limma was developed for microarrays and then adapted to RNA-Seq data, researchers also use it for proteomics data as they tend to have similar characteristics. In our first publications Mass Dynamics 1.0 (Section: MD 1.0 Reproduces Perseus Results Reliably on Sample Datasets) we show how by using limma we are able to reproduce the results obtained using Perseus, another established method for DE used in mass spectrometry, which is also parametric.
Please feel free to check out the limma user manual.