Diogo Borges Lima

© · Diogo Borges Lima
Munich, Germany

About

Research Scientist

I hold a Bachelor's degree in Computer Science from the Federal University of Rio de Janeiro (UFRJ), Brazil, and an M.Sc. in Computer Science specializing in Artificial Intelligence from UFRJ's Systems Engineering and Computer Science Program. I also hold a Ph.D. in Biosciences and Biotechnology from the Carlos Chagas Institute / Fiocruz, where I developed SIM-XL, a search tool for complex cross-linked peptide scenarios that supports structural proteomics and protein–protein interaction studies.

During my first postdoc in computational proteomics at Institut Pasteur in Paris, I built new bioinformatics solutions for top-down proteomics data. In my second postdoc at the Leibniz-FMP in Berlin, I focused on cross-linking mass spectrometry data analysis using cleavable reagents and on tools to accelerate peptide identification.

Currently, I'm a Research Scientist in computational proteomics at Abbott Cancer Diagnostics in Munich, Germany.

Get in touch

Core expertise

Academic background

Education

Formal training spanning computer science, artificial intelligence, and bioinformatics — culminating in a doctoral thesis on cross-linked peptide identification.

Ph.D.

Bioinformatics and Computational Biology

Carlos Chagas Institute — Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil · 2013–2016

"Algorithm for identifying cross-linked peptides analyzed by mass spectrometry" (PDF, Portuguese)

Supervised by Dr. Paulo C. Carvalho and Dr. Fabio Cesar Gozzo. Developed SIM-XL, a new search engine for identifying and annotating cross-linked peptides. Watch the demo →

M.Sc.

Computer Science and Systems Engineering

COPPE — Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil · 2011–2013

"Computational method for identifying peptides labeled with phenylisothiocyanate analyzed by LC-MS/MS" (PDF, Portuguese)

Supervised by Dr. Paulo C. Carvalho and Dr. Felipe M. G. França. Developed SIM (Spectrum Identification Machine), a mass spectrometry search tool using a PSM approach.

B.Sc.

Computer Science

DCC — Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil · 2006–2010

"Redução do Acoplamento com Frameworks Específicos de Plataforma no MDArte: Estudo de Caso em Ambientes Móveis" (PDF, Portuguese)

Linguistic abilities

PTPortuguese Native

ENEnglish Advanced

FRFrench Advanced

DEGerman Intermediate

ESSpanish Basic

Full resume

Curriculum Vitae

Download PDF Lattes CV

Experience

Research Scientist

Abbott Cancer Diagnostics (formerly Exact Sciences)

Munich, Germany · Since Sep 2024

Postdoc — Computational Proteomics, Cross-linking Mass Spectrometry

The Liu Lab — Leibniz-FMP

Berlin, Germany · 2020–2024

Supervised by Dr. Fan Liu. Co-developed Scout for identifying and quantifying cross-linked peptides using cleavable reagents.

Data Scientist in Proteomics

Winter Lab — CeMM

Vienna, Austria · Jan–Aug 2020

Postdoc — Bioinformatics and Computational Biology

Institut Pasteur — Mass Spectrometry for Biology Unit

Paris, France · 2016–2019

Supervised by Dr. Julia Chamot-Rooke. Developed an algorithm for top-down proteomics data analysis.

Ph.D. — Bioinformatics and Computational Biology

Carlos Chagas Institute — Fiocruz

Curitiba, Brazil · 2013–2016

Developed SIM-XL, a search engine for identifying and annotating cross-linked peptides.

M.Sc. — Computer Science and Systems Engineering

COPPE — Federal University of Rio de Janeiro (UFRJ)

Rio de Janeiro, Brazil · 2011–2013

Honors & Awards

Honorable mention, "Prêmio Capes de Tese 2016" — top 3 PhD theses in biological sciences in Brazil, October 2017
One of the best projects presented in the academic journey — ICC/Fiocruz, 2014 & 2015
Best poster, Masters category — BrProt Conference, 2012

Journal Reviewer

Bioinformatics
Scientific Reports — Nature
Journal of Proteomics
Biochimica et Biophysica Acta — Proteins and Proteomics
Letters in Drug Design & Discovery
ECCB — International Society for Computational Biology
Source Code for Biology and Medicine — BMC

Details & involvement

Co-supervisor of MSc and PhD students

Louise Ulrich Kurt, PhD in Biosciences and Biotechnology, ICC/Fiocruz, Brazil (2024)
Milan Avila Clasen, PhD in Biosciences and Biotechnology, ICC/Fiocruz, Brazil (2023)
Louise Ulrich Kurt, MSc in Biosciences and Biotechnology, ICC/Fiocruz, Brazil (2020)
Milan Avila Clasen, MSc in Biosciences and Biotechnology, ICC/Fiocruz, Brazil (2019)

Supervisor of undergraduate students (BSc)

André Ramos Fernandes da Silva, BSc Computer Science, UFRJ, Brazil (2014)
Felipe Araújo Teixeira, BSc Computer Science, UFRJ, Brazil (2014)
Lucas Henning Brisola, BSc Biomedical Informatics, UFPR, Brazil (2014)
Marcos Antonio Serpa de Barros, BSc Computer Science, UFRJ, Brazil (2014)

Invited lectures & seminars in computational proteomics

XII Proteomics Workshop (virtual), Campinas, Brazil — Oct 30–Nov 1, 2023
International Course on Proteome Analysis by MS, Institut Pasteur de Montevideo, Uruguay — Mar 21–30, 2022 (54h)
Top-down Proteomics course, 7th Brazilian Conference on Mass Spectrometry, Rio de Janeiro — Dec 7, 2018 (9h)
International Course on Proteome Analysis by MS, Institut Pasteur de Montevideo, Uruguay — Oct 15–23, 2018 (54h)
Séminaire, Journées Departamentales DBSC, Institut Pasteur, Paris — Dec 12–13, 2017
Séminaire DBSC, Institut Pasteur, Paris — Feb 14, 2017
International Course on Proteome Analysis by MS, Institut Pasteur de Montevideo, Uruguay — Nov 28–Dec 2, 2016 (35h)
VII Proteomics Workshop, Campinas, Brazil — Nov 10–11, 2016 (15h)
VI BrMass & 1st IbMS course: Proteomics, Rio de Janeiro — Dec 9, 2016 (8h)

Events organization

Symposium in Proteomics, Fiocruz, Rio de Janeiro — Nov 7, 2014
1st Symposium Carlos Chagas Institute in Proteomics, Curitiba — Jul 5, 2013

Conference & event participation (2012–2023)

71^st American Society for Mass Spectrometry. Houston, USA. June 4^th to 8^th, 2023 - ASMS (Conference).
Berlin PostDoc day 2022. Berlin, Germany. November 3^rd, 2022 - PostDoc Day 2022 (Symposium).
70^th American Society for Mass Spectrometry. Minneapolis, USA. June 5^th to 9^th, 2022 - ASMS (Conference).
Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. March 21^st to 30^th, 2022 - International Course - IP Montevideo (Course).
X Proteomics Workshop. (virtual). November 3^rd to 5^th, 2021 - Workshop LNBio (Symposium).
Berlin PostDoc day 2021. Berlin, Germany. November 4^th, 2021 - PostDoc Day 2021 (Symposium).
Berlin PostDoc day 2020. Berlin, Germany. November 13^th, 2020 - PostDoc Day 2020 (Symposium).
1^st European Top-down Proteomics Symposium. Paris, France. February 12^th to 14^th, 2019 - 1^st EuTDP (Symposium).
7^th BrMass. Rio de Janeiro, RJ. December 8^th to 12^th, 2018 - BrMass (Conference).
Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. October 15^th to 23^rd, 2018 - International Course - IP Montevideo (Course).
66^th American Society for Mass Spectrometry. San Diego, USA. June 3^rd to 7^th, 2018 - ASMS (Conference)
Departmental Days of the Department of Structural Biology and Chemistry - Institut Pasteur. Paris, France. December 12^th and 13^th, 2017 (Departamental Journey).
São Paulo School of Advanced Science on Mass Spectrometry - based Proteomics - SPSAS-MS. Campinas, Brazil. August 28^th to September 6^th, 2017 - SPSAS-MS (Workshop)
65^th American Society for Mass Spectrometry. Indianapolis, USA. June 4^th to 8^th, 2017 - ASMS (Conference)
VI BrMass & 1^st IbMS. Rio de Janeiro, RJ. December 10^th to 14^th - 6^th, 2016 - BrMass (Conference).
Proteome Analysis by Mass Spectrometry. Montevideo, Uruguay. November 28^th to December 2^nd, 2016 - International Course - IP Montevideo (Course).
VII Proteomics Workshop. Campinas, SP. November 8^th to 11^th, 2016 - Workshop LNBio (Symposium).
2nd Proteomics meeting of the Brazilian Proteomics Society. Buzios, RJ. December 7^th to 10^th - 2^nd, 2014 - BrProt (Conference)
V BrMass. Campinas, SP. December 7^th to 11^th - 5^th, 2013 - BrMass (Conference).
IV Proteomics Workshop. Campinas, SP. November 6^th and 7^th, 2013 - Workshop LNBio (Symposium).
Advanced topics in Proteomics. Rio de Janeiro, RJ. From October, 29^th to November 1^st, 2013 (Symposium).
1st Symposium Carlos Chagas Institute in Proteomics. Curitiba, PR. July 5^th, 2013 (Symposium)
São Paulo Advanced School on Bioorganic Chemistry. Araraquara, SP. July 1^st to 5^th, 2013 - ESPCA (Conference)
Implementation and Perspectives of MS-Imaging in Rio de Janeiro, RJ. June 6^th and 7^th, 2013 - MSI 2013 - Rio (Symposium)
1^st National Meeting of Brazilian Proteomics Society. Rio de Janeiro, RJ. December 10^th, 11^th and 12^th, 2012 - BrProt (Conference)
V Proteomics Forum of Rio de Janeiro. November 29^th and 30^th, 2012 (Conference)
III Proteomics Workshop. Campinas, SP. November 8^th, 2012 - Workshop LNBio (Symposium).

Technical skills

Hobbies

Peer-reviewed & more

Publications

A complete record of journal articles, preprints, book chapters, software deposits and a patent spanning structural proteomics, top-down MS, and cross-linking mass spectrometry.

Focus areas

Research Interest

My work sits at the intersection of structural biology, computational proteomics, and artificial intelligence — building the algorithms that make complex mass spectrometry data interpretable.

Computational Proteomics

Targeted Proteomics

Structural Biology
Cross-linking MS

Artificial Intelligence

Software tools in computational proteomics

Scout SIM-XL RawVegetable 2.0 Q2C TDFragMapper XlinkCyNET ProteoCombiner Top-Down Garbage Collector DiagnoProt PatternLab

Get in touch

Contact

Abbott Cancer Diagnostics
(formerly Exact Sciences) Munich, Germany

Currently based in Munich, working on computational proteomics for cancer diagnostics research.