Fig. 2: RAPDOR workflow.
From: RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
The RAPDOR tool converts analyzed mass spectrometry data with x fractions from n replicates and two conditions into probability distributions. It continues with the calculation of the relative entropy (relEntr) and the Shannon entropy. It uses the Jensen-Shannon distance (\({JSD}\)) between all pairwise samples to carry out an ANOSIM and evaluates the effect size via the \({JSD}\) between the mean distributions of the conditions. Lastly, distribution changes are visualized in an interactive web server displaying several parameters such as the relative position shift (RSD) and the relative distribution change (RDC). Depending on the number of replicates, the individual proteins can be either tested for redistribution using ANOSIM or ranked according to their assigned ANOSIM \(R\) values.
