The first release of the Neopeptide Analyser tool, with the Open Source MIT licence added. This tool takes two inputs - the exported output from Progenesis QIP and a fasta file giving a protein 'database'. The tool produces two outputs - firstly, a modified version of the Progenesis QIP output, with additional columns marking those peptides that are fully tryptic (and hence the neopeptides can be filtered), and optionally the previous and next residues from the associated protein. The second output file gives normalised values for the neopeptide abundances as well as statistics describing the significance of the abundance changes across the two conditions (according to the Progenesis QIP input file). To use the tool, download the NeopeptideTool.jar and open it (on any system with Jave SE version 7 runtime environment installed). No external libraries are needed to compile the source.