The PRIDEConverter software enables conversion from a variety of mass spectra and search engine file formats into the PRIDE XML format that can subsequently be used for uploading spectra and peptide/protein identifications into the PRIDE database . However, the PRIDEConverter has been designed primarily for "shotgun proteomics" experimental designs, where peptide to protein inference is performed across all input spectra, which is not well suited to gel-based studies.

PRIDESpotMapper is a novel Java-based application that modifies any any PRIDE XML file generated using the PRIDEConverter dividing the identified proteins according to the source identification file for each gel spots. Starting from a PRIDE XML file and either an XML or Excel spot map (Go to download section to get an example) the application ensures that records are created for each identified protein, derived from peptide identifications from each input file independently.