Effectively addressing complex proteomic search spaces with peptide spectrum matching. - Diogo B. Lima; Yasset Pérez-Riverol; Fabio C. S. Nogueira; Gilberto B. Domont; Jesus Noda; Felipe da Veiga Leprevost; Vladimir Besada; Felipe M. G. França; Valmir Carneiro Barbosa; Aniel Sánchez; Paulo C. Carvalho (Bioinform., 2013)

DiagnoProt: a tool for discovery of new molecules by mass spectrometry. - André Ramos Fernandes Da Silva; Diogo B. Lima; Alejandro Leyva; Rosario Durán; Carlos Batthyany; Priscila F. Aquino; Juliana C. Leal; Jimmy E. Rodriguez; Gilberto B. Domont; Marlon D. M. Santos; Julia Chamot-Rooke; Valmir C. Barbosa; et al. (Bioinform., 2017)

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)

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. - Louise U. Kurt; Milan A. Clasen; Marlon D. M. Santos; Eduardo S. B. Lyra; Luana O. Santos; Carlos H. I. Ramos; Diogo B. Lima; Fábio C. Gozzo; Paulo C. Carvalho (Bioinform., 2021)

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)

Increasing confidence in proteomic spectral deconvolution through mass defect. - Milan A. Clasen; Louise U. Kurt; Marlon D. M. Santos; Diogo B. Lima; Fan Liu; Fábio C. Gozzo; Valmir C. Barbosa; Paulo C. Carvalho (Bioinform., 2022)