Diogo Borges Lima


Publications

Publications in peer reviewed journals

  1. Alt text Louise Ulrich Kurt, Milan Avila Clasen, Ísis Venturi Biembengut, Max Ruwolt, Fan Liu, Fabio César Gozzo, Paulo Costa Carvalho, Diogo Borges Lima, “RawVegetable 2.0 – Refining XL-MS data acquisition through enhanced quality control”, Journal of Proteome Research: Special Issue: Women in Proteomics and Metabolomics (accepted), 2024.

  2. Alt text Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou-Nader, Christophe Velours, Yosra Zarrouk, Christophe Le Clainche, Christian Malosse, Diogo Borges Lima, Nicole Quenech’Du, Bilal Mazhar, Sami Essid, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmström, Guy Tran Van Nhieu, “Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint”, Cell Reports 42 (4): 112405, 2023.

  3. Alt text Milan A Clasen, Marlon D M Santos, Louise Ulrich Kurt, Juliana Fischer, Amanda C Camillo-Andrade, Lucas Albuquerque Sales, Tatiana de Arruda Campos Brasil de Souza, Diogo Borges Lima, Fabio C Gozzo, Richard Hemmi Valente, Rosario Duran, Valmir C Barbosa, Paulo C Carvalho, “PatternLab V handles multiplex spectra in shotgun proteomic searches and increases identification”, Journal of the American Society for Mass Spectrometry 34 (4): 794-796, 2023.

  4. Alt text Max Ruwolt, Yi He, Diogo Borges Lima, William Barshop, Johannes Broichhagen, Romain Huguet, Rosa Viner, Fan Liu, “Real-time library search increases cross-link identification depth across all levels of sample complexity”, Analytical Chemistry 95 (12): 5248–5255, 2023.

  5. Alt text Marlon D M Santos, Amanda C Camillo-Andrade, Diogo B Lima, Tatiana A C B Souza, Juliana S G Fischer, Richard H Valente, Fabio C Gozzo, Valmir C Barbosa, Carlos Batthyany, Julia Chamot-Rooke, Rosario Duran, Paulo C. Carvalho, “DiagnoMass: a proteomics hub for pinpointing discriminative spectral clusters”, Journal of Proteomics: (277): 104853, 2023.

  6. Alt text Milan A Clasen, Louise U Kurt, Marlon D M Santos, Diogo B Lima, Fan Liu, Fabio C Gozzo, Valmir C Barbosa, Paulo C Carvalho, “Increasing confidence in proteomic spectral deconvolution through mass defect”, Bioinformatics 38 (22): 5119-5120, 2022.

  7. Alt text Marlon D M Santos, Diogo B Lima, Juliana S G Fischer, Milan A Clasen, Louise U Kurt, Amanda Caroline Camillo-Andrade, Leandro C Monteiro, Priscila F de Aquino, Ana G C Neves-Ferreira, Richard H Valente, Monique R O Trugilho, Giselle V F Brunoro, Tatiana A C B Souza, Renata M. Santos, Michel Batista, Fabio C Gozzo, Rosario Durán, John R Yates, Valmir C Barbosa, Paulo C Carvalho, “Simple, efficient, and thorough shotgun proteomic analysis with PatternLab V”, Nature Protocols (17):1553–1578, 2022.

  8. Alt text Max Ruwolt, Lennart Schnirch, Diogo Borges Lima, Michal Nadler-Holly, Rosa Viner, Fan Liu, “Optimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies”, Analytical Chemistry 94 (13): 5265–5272, 2022.

  9. Alt text Barbara S. Soares, Surza Lucia G. Rocha, Viviane A. Bastos, Diogo B. Lima, Paulo C. Carvalho, Fábio César Gozzo, Borries Demeler, Tayler L. Williams, Janelle Arnold, Amy Henrickson, Thomas J. D, Jorgensen, Tatiana A. C. B. Souza, Jonas Perales, Richard H. Valente, Bruno Lomonte, Francisco Gomes-Neto, Ana Gisele C. Neves-Ferreira, “Molecular architecture of the antiophidic protein DM64 and its binding specificity to myotoxin II from Bothrops asper venom”, Frontiers in Molecular Biosciences - section: Structural Biology 8: 787368, 2022.

  10. Alt text Jonathan Dhenin, Diogo B Lima, Mathieu Dupré, Julia Chamot-Rooke, “TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics”, Bioinformatics 38 (4): 1136-1138, 2022.

  11. Alt text André R. F. Silva, Diogo B Lima, Louise U. Kurt, Mathieu Dupré, Julia Chamot-Rooke, Marlon D. M. Santos, Carolina Alves Nicolau, Richard Hemmi Valente, Valmir C. Barbosa, Paulo C. Carvalho, “Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra”, Journal of Proteomics: (245): 104282, 2021.

  12. Alt text Diogo B Lima, Mathieu Dupré, Marlon D. M. Santos, Paulo C. Carvalho, Julia Chamot-Rooke, “DiagnoTop: a computational pipeline for discriminating bacterial pathogens without database search”, Journal of the American Society for Mass Spectrometry 32 (6): 1295-1299, 2021.

  13. Alt text Diogo B Lima, Ying Zhu, Fan Liu, “XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications”, Journal of Proteome Research (20): 1943–1950, 2021.

  14. Alt text Louise U. Kurt, Milan A. Clasen, Marlon D. M. Santos, Eduardo S. B. Lyra, Luana O. Santos, Carlos H. I. Ramos, Diogo B Lima, Fabio C. Gozzo, Paulo C. Carvalho, “Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition”, Bioinformatics 37 (18): 3035-3037, 2021.

  15. Alt text Dupré, Mathieu; Duchateau, Magalie; Malosse, Christian; Lima, Diogo; Calvaresi, Valeria; Podglajen, Isabelle ; Clermont, Dominique; Rey, Martial; Chamot-Rooke, Julia, “Optimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination”, Journal of Proteome Research (20): 202-211, 2021.

  16. Alt text Diogo B Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke, “ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment”, Bioinformatics 37 (15): 2206-2208, 2021.

  17. Alt text Louise U Kurt, Milan A Clasen, Marlon D M Santos, Tatiana A C B Souza, Emanuella C Andreassa, Eduardo B Lyra, Diogo B Lima, Fabio C Gozzo, Paulo C Carvalho, “RawVegetable – A data assessment tool for proteomics and cross-linking mass spectrometry experiments”, Journal of Proteomics: (225) - Special Issue: Structural Proteomics: 103864, 2020.

  18. Alt text Giselle Villa Flor Brunoro, Rubem Menna-Barreto, Aline Garcia-Gomes, Carolina Boucinha, Diogo B Lima, Paulo Carvalho, André Teixeira-Ferreira, Monique R.O. Trugilho, Jonas Perales, Veit Schwämmle, Marcos Catanho, Ana Tereza Vasconcelos, Maria Cristina M Motta, Claudia Masini d'Avila Levy, “Quantitative proteomic map of the trypanosomatid Strigomonas culicis: The biological contribution of its endosymbiotic bacterium”, Protist 170 (6): 125698, 2019.

  19. Alt text Diogo B Lima, André R F 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, “Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra”, Bioinformatics 35 (18): 3489-3490, 2019.

  20. Alt text Marlon D M Santos, Diogo B Lima, André R F Silva, Louise U Kurt, Milan A Clasen, Antônio F M Pinto, James J. Moresco, John R Yates III, Priscila Aquino, Valmir C Barbosa, Juliana S G Fischer, Paulo C Carvalho, “A quantitation module for isotope-labeled peptides integrated into Patternlab for Proteomics”, Journal of Proteomics (202): 103371, 2019.

  21. Alt text Chuanlong Cui, Tong Liu, Tong Chen, Johanna Lu, Ian Casaren, Diogo Borges Lima, Paulo Costa Carvalho, Annie Beuve and Hong Li, “Comprehensive Identification of Protein Disulfide Bonds with Pepsin/Trypsin Digestion, Orbitrap HCD and Spectrum Identification Machine”, Journal of Proteomics (198): 78-86, 2019.

  22. Alt text Marcelle A.Caminha, Virginia Maria B.de Lorena, Wilson de Oliveira Júnior, Jonas Perales, Paulo C.Carvalho, Diogo B Lima, Maria da Glória A.M.Cavalcanti, Sílvia M.Martins, Richard H.Valente, Rubem F.S.Menna-Barreto, “Trypanosoma cruzi immunoproteome: Calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy”, Journal of Proteomics (194): 179-190, 2019.

  23. Alt text Marcelle A Caminha; Virginia Maria B Lorena; Wilson Oliveira Jr; Jonas Perales; Paulo C Carvalho; Diogo B Lima; Maria da Glória A Cavalcanti; Sílvia M Martins; Richard H Valente; Rubem Figueiredo Sadok Menna Menna-Barreto, “Data on antigen recognition hindrance by antibodies covalently immobilized to Protein G magnetic beads by dimethyl pimelimidate (DMP) cross-linking”, Data in brief (22): 516-521, 2019.

  24. Alt text Fioramonte, Mariana; de Jesus, Hugo; Ferrari, Allan; Lima, Diogo; Drekener, Roberta; Correia, Carlos Roque; Oliveira, Luciana; Neves-Ferreira, Ana; Carvalho, Paulo; Gozzo, Fabio, “XPlex: an effective, multiplex cross-linking chemistry for acidic residues”, Analytical Chemistry 90 (10): 6043–6050, 2018.

  25. Alt text Lima, D.B.; Melchior, J. T.; Morris, J.; Barbosa, V. C.; Chamot-Rooke, J.; Gozzo, F. C.; Souza, T. A. C. B.; Fischer, J. S. G.; Carvalho, P. C.; Davidson, W. S., “Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins”, Nature Protocols (13): 431–458, 2018.

  26. Alt text André R F Silva, Diogo B Lima, Alejandro Peña, Rosario Duran, Carlos Batthyany, Priscila F Aquino, Juliana C Leal, Jimmy E Rodriguez, Gilberto B Domont, Marlon D M Santos, Julia Chamot-Rooke, Valmir C Barbosa, and Paulo C Carvalho, “DiagnoProt: a tool for discovery of new molecules by mass spectrometry”, Bioinformatics 33 (12): 1883-1885, 2017.

  27. Alt text Melchior, J.T., Walker, R.G., Morris, J., Jones, M.K., Segrest J.P., Lima, D.B., Carvalho, P.C., Gozzo, F.C., Castleberry, M., Thompson, T.B., W. Sean Davidson, “An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding”, The Journal of Biological Chemistry (291): 5439-5451, 2016.

  28. Alt text Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost, Marlon M Dias, Juliana S G Fischer, Priscila F Aquino, James J Moresco, John R Yates III, Valmir C Barbosa, “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”, Nature Protocols (11): 102-117, 2016.

  29. Alt text Diogo B Lima, Tatiani B de Lima, Tiago S Balbuena, Ana Gisele C. Neves-Ferreira, Valmir C Barbosa, Fabio C Gozzo, Paulo C. Carvalho, “SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis”, Journal of Proteomics (129) - Special Issue: Computational Proteomics: 51-55, 2015.

  30. Alt text Priscila Ferreira Aquino, Diogo Borges Lima, Juliana de Saldanha da Gama Fischer, Rafael Donadélli Melani, Fabio C S Nogueira, Sidney R S Chalub, Elzalina R. Soares, Valmir C Barbosa, Gilberto B. Domont, Paulo C. Carvalho, “Exploring the proteomic landscape of a gastric cancer biopsy with the Shotgun Imaging Analyzer”, Journal of Proteome Research (13): 314-320, 2014.

  31. Alt text Felipe V. Leprevost, Richard H. Valente, Diogo Borges, Jonas Perales, Rafael Melani, John R. Yates III, Valmir C. Barbosa, Magno Junqueira, and Paulo C. Carvalho, “PepExplorer: a similarity-driven tool for analyzing de novo sequencing results”, Molecular & Cellular Proteomics 13: 2480–2489, 2014.

  32. Alt text Lima, Daniel C ; Duarte, Fábio T ; Medeiros, Viviane ; Lima, Diogo B ; Carvalho, Paulo ; Bonatto, Diego ; Batistuzzo de Medeiros, Silvia R, “The influence of iron on the proteomic profile of Chomobacterium violaceum”, BMC Microbiology (14): 267, 2014.

  33. Alt text Diogo Borges, Yasset Perez-Riverol, Fabio C. S. Nogueira, Gilberto B. Domont, Jesus Noda, Felipe da Veiga Leprevost, Vladimir Besada, Felipe M. G. França, Valmir C. Barbosa, Aniel Sánchez, and Paulo C. Carvalho, “Effectively addressing complex proteomic search spaces with peptide spectrum matching”, Bioinformatics (29) 10: 1343-1344, 2013.

  34. Alt text Daniela F. S. Chaves, Paulo C. Carvalho, Diogo B Lima, Humberto Nicastro, Fabio M Lorenzeti, Mario S. Filho, Sandro M Hirabara, Paulo H.M. Alves, James J Moresco, John R. Yates, Antonio H. Lancha, “Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry”, Journal of Proteome Research 12 (10): 4532–4546, 2013.

  35. Alt text Felipe da Veiga Leprevost, Diogo Borges Lima, Juliana Crestani, Yasset Perez-Riverol, Nilson Zanchin, Valmir C. Barbosa, Paulo Costa Carvalho, “Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics”, Journal of Proteomics (89): 179-182, 2013.

  36. Alt text Yasset Perez-Riverol, Aniel Sanchez, Jesus Noda, Diogo Borges, Paulo Costa Carvalho, Rui Wang, Juan Antonio Vizcaíno, Lazaro Hiram Betancourt, Yassel Ramos, Gabriel Duarte, Fabio C.S. Nogueira, Luis Javier Gonzalez, Gabriel Padron, David Lee Tabb, Henning Hermjakob, Gilberto B. Domont, and Vladimir Besada, “HI-bone: A scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and High Intensity fragment ions.”, Analytical Chemistry 85 (7): 3515–3520, 2013.

Unreferenced preprint publications

  1. Alt text Milan Avila Clasen*, Max Ruwolt*, Louise U. Kurt, Fabio C Gozzo, Shuai Wang, Tao Chen, Paulo C Carvalho#, Diogo Borges Lima#, Fan Liu#, "Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics", bioRxiv, 2023.

  2. Alt text Max Ruwolt, Yi He, Diogo Borges Lima, William Barshop, Johannes Broichhagen, Romain Huguet, Rosa Viner, Fan Liu, “Real-time library search increases cross-link identification depth across all levels of sample complexity”, bioRxiv, 2022.

  3. Alt text Ying Zhu, Kerem Can Akkaya, Diogo Borges Lima, Cong Wang, Martin Lehmann, Fan Liu, “Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology”, bioRxiv, 2022.

  4. Alt text Jonathan Dhenin, Diogo Borges Lima, Mathieu Dupré, Julia Chamot-Rooke, “TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics”, bioRxiv, 2021.

  5. Alt text Diogo Borges Lima, Jonathan Dhenin, Mathieu Dupré, Julia Chamot-Rooke, “Using TDFragMapper: a high-performance tool to assess experimental parameters in top-down proteomics”, Nature Protocol Exchange, 2021.

  6. Alt text Diogo Borges Lima, Ying Zhu, Fan Liu, “XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications”, bioRxiv, 2020.

  7. Alt text Diogo Borges Lima, Ying Zhu, Fan Liu, “Using XlinkCyNET to visualize protein cross-links in Cytoscape software”, Nature Protocol Exchange, 2020.

  8. Alt text Diogo Borges Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke, “Using ProteoCombiner to integrate bottom-up and top-down proteomics data to improve proteoform identification”, Nature Protocol Exchange, 2020.

  9. Alt text Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Charles Bou-Nader, Christian Malosse, Diogo Borges Lima, Chakir Bello, Benjamin Cocom-Chan, Nicole Quenech’Du, Bilal Mazhar, Delphine Javelaud, Jacques Fattaccioli, Alain Mauviel, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmström, Guy Tran Van Nhieu “Vinculin targeting by Shigella IpaA promotes stable cell adhesion independent of mechanotransduction”, bioRxiv, 2019.

  10. Alt text Francisco Gomes Neto, Barbara S Soares, Surza LG Rocha, Diogo B Lima, Fabio C Gozzo, Jonas Perales, Bruno Lomonte, Richard H Valente, Ana Gisele C Neves-Ferreira “Modeling Protein-Protein Interactions: a structural insight of myotoxin-antimyotoxin complex based on cross-linking data, resolved by mass spectrometry”, Toxicon (168 - Supplement 1): S27, 2019.

  11. Alt text Barbara Silva Soares; Surza Lucia Gonçalves da Rocha; Diogo Borges Lima; Mariana Fioramonte; Fabio Cesar Gozzo; Bruno Lomonte; Richard Hemmi Valente; Francisco Gomes-Neto; Ana Gisele da Costa Neves Ferreira; Jonas Perales “Structural analysis of a myotoxin-antimyotoxin complex by cross-linking, mass spectrometry, and bioinformatics”, Toxicon (158 - Supplement 1): S29-S30, 2019.

  12. Alt text Diogo B Lima, Tatiani B de Lima, Tiago S Balbuena, Ana Gisele C. Neves-Ferreira, Valmir C Barbosa, Fabio C Gozzo, Paulo C. Carvalho, “Using SIM-XL to identify and annotate cross-linked peptides analyzed by mass spectrometry”, Nature Protocol Exchange, 2015.

Book chapter published

  1. Alt text Gault, Joseph ; Vorontsov, Egor ; Dupré, Mathieu ; Calvaresi, Valeria ; Duchateau, Magalie ; Lima, Diogo B. ; Malosse, Christian ; Chamot-Rooke, Julia, “Top-Down Proteomics in the Study of Microbial Pathogenicity”, MALDI-TOF and Tandem MS for Clinical Microbiology, John Wiley & Sons, Ltd, 2017, p. 493-504.

Software deposits

  1. Alt text Chamot-Rooke, J.; Lima, D.B.; Dhenin, J; Dupré, M.; TDFragMapper version 1.0 2021, France. Privilege of innovation. Register number: IDDN.FR.001.080039.000.S.C.2021.000.31235, institution of registration: Agence pour la Protection des Programmes, Depositor: Chamot-Rooke, J.; Institut Pasteur, Deposit: 02/23/2021

  2. Alt text Chamot-Rooke, J.; Lima, D.B.; Dupré, M.; Duchateau, M; Giai-Gianetto, Q.; Rey, M.; Mattondo, M. ProteoCombiner version 1.0 2019, France. Privilege of innovation. Register number: IDDN.FR.001.410008.000.S.C.2019.000.31235, institution of registration: Agence pour la Protection des Programmes, Depositor: Chamot-Rooke, J.; Institut Pasteur, Deposit: 01/10/2019

Patent

  1. Alt text Carvalho, P.C.; Barbosa, V.C.; Lima, D.B.; Silva, A. R. F.; Batthyany, C.; Duran, R.; Chamot-Rooke, J.; Leyva, A. P. System, method and device for identifying discriminant biological factors and for classifying proteomic profiles. 2016, USA. Privilege of innovation. Register number: 62422964, institution of registration: United States patent and Trademark Office, Depositors: Carvalho, P.C.; Institut Pasteur; Instituto Pasteur de Montevideo, Deposit: 17/11/2016