Other ; This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/bioinformatics/btw580 ; Abstract ; $\textbf{Summary:}$ DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis signifi- cance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser. $\textbf{Availability and implementation:}$ DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages. $\textbf{Contact:}$ samuel.wieczorek@cea.fr, florence.combes@cea.fr, thomas.burger@cea.fr ; Other ; ANR-2010-GENOM-BTV-002-01 (ChloroTypes), ANR-10-INBS-08 (ProFI project, ‘Infrastructures Nationales en Biologie et Sante´’, ‘Investissements d’Avenir’), European Union FP7 program (Prime-XS Project, Contract no. 262067), Prospectom project (Mastodons 2012 CNRS Challenge), Biotechnology and Biological Sciences Research Council (Strategic Longer and Larger Grant ID: BB/L002817/1)