Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra. - Diogo B. Lima; André Ramos Fernandes Da Silva; Mathieu Dupré; Marlon D. M. Santos; Milan A. Clasen; Louise U. Kurt; Priscila F. Aquino; Valmir C. Barbosa; Paulo C. Carvalho; Julia Chamot-Rooke (Bioinform., 2019)

ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. - Diogo B. Lima; Mathieu Dupré; Magalie Duchateau; Quentin Giai Gianetto; Martial Rey; Mariette Matondo; Julia Chamot-Rooke (Bioinform., 2021)

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics. - Jonathan Dhenin; Diogo B. Lima; Mathieu Dupré; Julia Chamot-Rooke (Bioinform., 2022)