Recent improvements in proteomic technologies have collectively yielded data sets that far exceed the capabilities of typical low-throughput interpretation strategies. Unfortunately, tools designed to leverage the "peptide-centric" content of MS-based proteomics lag the current rate of data production. Here, we describe Pathway Palette (http://blaispathways.dfci.harvard.edu), a freely accessible internet application that enables researchers to easily transition from peptides to biological pathways, while simultaneously retaining the qualitative and quantitative aspects of the underlying MS data.