D. B. Lima

发表

Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins

Diogo B Lima, Paulo C Carvalho, Juliana S G Fischer, 2018, Nature Protocols.

Vinculin targeting by Shigella IpaA promotes stable cell adhesion independent of mechanotransduction

Lars Malmström, Hamed Khakzad, M. Fontecave, 2019, bioRxiv.

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology

Martin Lehmann, D. B. Lima, Ying Zhu, 2022, bioRxiv.

XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

Fan Liu, D. B. Lima, Ying Zhu, 2020, bioRxiv.

The influence of iron on the proteomic profile of Chromobacterium violaceum

D. Bonatto, P. Carvalho, D. B. Lima, 2014, BMC Microbiology.

Top‐Down Proteomics in the Study of Microbial Pathogenicity

C. Malosse, J. Chamot-Rooke, J. Gault, 2017 .

Using SIM-XL to identify and annotate cross-linked peptides analyzed by mass spectrometry

V. Barbosa, F. Gozzo, P. Carvalho, 2015 .

Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry.

J. Yates, S. Hirabara, J. Moresco, 2013, Journal of proteome research.

RawVegetable - A data assessment tool for proteomics and cross-linking mass spectrometry experiments.

Marlon D. M. Santos, Milan A. Clasen, F. Gozzo, 2020, Journal of proteomics.

Using ProteoCombiner to integrate bottom-up and top-down proteomics data to improve proteoform identification

Martial Rey, J. Chamot-Rooke, Q. Gianetto, 2020 .

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

John R Yates, Diogo B Lima, Paulo C Carvalho, 2015, Nature Protocols.

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition

Fábio C. Gozzo, Paulo C. Carvalho, Diogo B. Lima, 2021, Bioinform..

Quantitative Proteomic Map of the Trypanosomatid Strigomonas culicis: The Biological Contribution of its Endosymbiotic Bacterium.

V. Schwämmle, M. Catanho, A. T. R. de Vasconcelos, 2019, Protist.

Comprehensive identification of protein disulfide bonds with pepsin/trypsin digestion, Orbitrap HCD and Spectrum Identification Machine.

Hong Li, Chuanlong Cui, Tong Liu, 2019, Journal of proteomics.

Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom

F. Gozzo, B. Lomonte, T. Jørgensen, 2022, Frontiers in Molecular Biosciences.

ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment

Diogo B Lima, Julia Chamot-Rooke, Quentin Giai Gianetto, 2020, Bioinform..

Trypanosoma cruzi immunoproteome: Calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy.

R. Menna-Barreto, P. Carvalho, J. Perales, 2019, Journal of proteomics.

SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis.

Diogo B Lima, Tatiani B de Lima, Tiago S Balbuena, 2015, Journal of proteomics.

DiagnoProt: a tool for discovery of new molecules by mass spectrometry

Gilberto B. Domont, Julia Chamot-Rooke, Valmir C. Barbosa, 2017, Bioinform..

Shigella ipaA mediates actin bundling through diffusible vinculin oligomers with activation imprint

Hamed Khakzad, M. Fontecave, N. Quenech’du, 2022, bioRxiv.

Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer.

Priscila F. Aquino, V. Barbosa, P. Carvalho, 2014, Journal of proteome research.

Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

Marlon D. M. Santos, Milan A. Clasen, V. Barbosa, 2022, Nature Protocols.

An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding*

F. Gozzo, R. G. Walker, J. Segrest, 2016, The Journal of Biological Chemistry.

PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results *

John R Yates, Diogo B Lima, Paulo C Carvalho, 2014, Molecular & Cellular Proteomics.

Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity

R. Huguet, R. Viner, D. B. Lima, 2022, bioRxiv.

XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues.

Allan J. R. Ferrari, F. Gozzo, C. R. Correia, 2018, Analytical chemistry.

ipaA triggers vinculin oligomerization to strengthen cell adhesion during Shigella invasion

Hamed Khakzad, M. Fontecave, N. Quenech’du, 2019 .

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.

P C Carvalho, V. Barbosa, P. Carvalho, 2013, Journal of proteomics.

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics

J. Chamot-Rooke, D. B. Lima, Mathieu Dupré, 2021, bioRxiv.

Using XlinkCyNET to visualize protein cross-links in Cytoscape software

D. B. Lima, Ying Zhu, Fan Liu, 2020 .

Shigella ipaA mediates actin bundling through diffusible vinculin oligomers with activation imprint

Hamed Khakzad, M. Fontecave, N. Quenech’du, 2022, bioRxiv.

SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis.

Tatiani B de Lima, V. Barbosa, F. Gozzo, 2015, Journal of proteomics.

PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification.

Marlon D. M. Santos, V. Barbosa, F. Gozzo, 2023, Journal of the American Society for Mass Spectrometry.