Diogo Borges Lima


Curriculum Vitae

Brazilian Lattes CV
Pasteur CV

Awards

  • One of the best project presented in the academic journey - ICC/Fiocruz - 2015
  • One of the best project presented in the academic journey - ICC/Fiocruz - 2014
  • The best poster in the Masters category - BrProt (Conference) - 2012

Events organization

  • Symposium in Proteomics at Fiocruz. Rio de Janeiro, RJ - Brazil. November 7th, 2014 (Symposium)
  • 1st Symposium Carlos Chagas Institute in Proteomics. Curitiba, PR - Brazil. July 5th, 2013 (Symposium)

Participation in events

2017

  • São Paulo School of Advanced Science on Mass Spectrometry - based Proteomics - SPSAS-MS. Campinas, Brazil. August 28th to September 6th - SPSAS-MS (Workshop)
  • 65th American Society for Mass Spectrometry. Indianapolis, USA. June 4th to 8th - 65th ASMS (Conference)

2016

  • VI BrMass & 1st IbMS. Rio de Janeiro, RJ. December 10th to 14th - 6th BrMass (Conference).
  • Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. November 28th to December 2nd - International Course - IP Montevideo (Course).
  • VII Proteomics Workshop. Campinas, SP. November 8th to 11th - Workshop LNBio (Symposium).

2014

  • 2nd Proteomics meeting of the Brazilian Proteomics Society. Buzios, RJ. December 7th to 10th - II BrProt (Conference)

2013

  • V BrMass. Campinas, SP. December 7th to 11th - 5th BrMass (Conference).
  • IV Proteomics Workshop. Campinas, SP. November 6th and 7th - Workshop LNBio (Symposium).
  • Advanced topics in Proteomics. Rio de Janeiro, RJ. From October, 29th to November 1st (Symposium).
  • 1st Symposium Carlos Chagas Institute in Proteomics. Curitiba, PR. July 5th (Symposium)
  • São Paulo Advanced School on Bioorganic Chemistry. Araraquara, SP. July 1st to 5th - ESPCA (Conference)
  • Implementation and Perspectives of MS-Imaging in Rio de Janeiro, RJ. June 6th and 7th - MSI 2013 - Rio (Symposium)

2012

  • 1st National Meeting of Brazilian Proteomics Society. Rio de Janeiro, RJ. December 10th, 11th and 12th - BrProt (Conference)
  • V Proteomics Forum of Rio de Janeiro. November 29th and 30th (Conference)
  • III Proteomics Workshop. Campinas, SP. November 8th - Workshop LNBio (Symposium).

Publications in peer reviewed journals

  1. 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., “Characterizing homodimer interfaces with cross-linking mass spectrometry and isotopically-labeled proteins”, Nature Protocols: to appear, 2017.

  2. 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 (2017) 33 (12): 1883-1885, 2017.

  3. 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): pp 5439-5451, 2016.

  4. 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).

  5. 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.

  6. 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).

  7. 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), pp 314-320, 2014.

  8. 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.

  9. 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, v. 14, p. 267, 2014.

  10. 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.

  11. 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), pp 4532–4546, 2013.

  12. 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.

  13. 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), pp 3515–3520, 2013.

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.

Reviewer of the following journal

  • Journal of Proteomics

Courses

  • Cellular and Molecular Biology - Oswaldo Cruz Institute/Fiocruz
  • Training Application in the LTQ Orbitrap XL ETD and LTQ Orbitrap Velos mass spectrometer, manufactured by Thermo Scientific company - Proteomics Unit / IQ - UFRJ
  • Operational Training in the LTQ Orbitrap XL ETD and LTQ Orbitrap Velos mass spectrometer, manufactured by Thermo Scientific company - Proteomics Unit / IQ - UFRJ
  • Introduction to Proteomics Technology: Key Concepts and Techniques Used - Oswaldo Cruz Institute/Fiocruz
  • Proteomic Data Analysis and Quantitative Mass Spectrometry - Oswaldo Cruz Institute/Fiocruz

Supervisor of undergraduate students (BSc)

Professional Experience

  • System development at Provisions Department of Brazil Navy (DAbM), SOMAR Project (SINGRA). (2009-2011)
  • System development at Federal Service of Data Processing (SERPRO), SICONV Project. (10/2008-2009)
  • System development at Cataloging Center of the Armed Force of Brazil Navy (CECAFA), I18N Project. (04/2008 ~ 10/2008)

Skills

  • Operating Systems: Linux, Unix, MacOS and Windows
  • Programming language: C, C#, C++, Java SE, Java EE, Java ME, J2ME, SQL, HTML, Javascript, XML, Prolog
  • Databases: MySQL, Oracle