Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/14251
Title: SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis
Authors: Lima, Diogo B.
Lima, Tatiani B. de
Balbuena, Tiago S.
Ferreira, Ana Gisele C. Neves
Barbosa, Valmir C.
Gozzo, Fábio C.
Carvalho, Paulo C.
Affilliation: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica e Engenharia de Proteínas. Paraná, Brasil
Universidade Estadual de Campinas. Laboratório Dalton de Espectrometria de Massas. Campinas, SP, Brasil.
Universidade Estadual de São Paulo (UNESP). Escola de Ciências Agrícolas e Veterinárias. Jaboticabal, SP, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.
Universidade Federal do Rio de Janeiro. Programa de Ciência da Computação e Engenharia de Sistemas
Universidade Estadual de Campinas. Laboratório Dalton de Espectrometria de Massas. Campinas, SP, Brasil.
Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica e Engenharia de Proteínas. Paraná, Brasil.
Abstract: Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics.
Keywords: Cross-linked
Cross-linking
Protein–protein
Issue Date: 2015
Publisher: Elsevier
Citation: LIMA, Diogo B. et al. SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. Journal of Proteomics, v.129, n.3, p.51-55, Nov. 2015.
DOI: 10.1016/j.jprot.2015.01.013
ISSN: 1874-3919
Copyright: restricted access
Appears in Collections:IOC - Artigos de Periódicos

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