SIM-XL: a tool for identifying cross
Transcrição
SIM-XL: a tool for identifying cross
Sociedade Brasileira de Espectrometria de Massas – BrMASS PRO – PROTEINS AND PEPTIDES SIM-XL: a tool for identifying cross-linked peptides in complex protein mixtures Diogo B Lima1, Tatiani Brenelli Lima2, Ana Gisele Neves Ferreira3, Valmir C Barbosa4, Tiago S Balbuena5, Fabio Cesar Gozzo2*, Paulo Costa Carvalho1* Corresponding: [email protected]; [email protected] 1. Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná 2. Dalton Mass Spectrometry Laboratory, IQ-Unicamp, Campinas-SP 3. Laboratory for Toxinology, Fiocruz, Rio de Janeiro 4. Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro 5. Laboratório de Proteômica Vegetal, Universidade Estadual Paulista, Jaboticabal-SP State of the art structural mass spectrometry based proteomics is often accomplished by using cross-linkers to covalently bind two or more reactive groups. This strategy is complementary to classical structural biology and therefore broadens the toolset for analyzing protein and protein-protein complex structures. One of the greatest challenges in identifying cross-linked peptides in complex protein mixtures is computationally dealing with the large search space which grows exponentially with each peptide included in the sequence database. Here, we present the preliminary results of an algorithm to deal with this problem termed Spectrum Identification Machine for Cross-Linked peptides (SIM-XL). It capitalizes on experimental features that allow us to effectively address the massive combinatorial problem at hand. We evaluated our method in a gold standard proteomic complex dataset by first using a sequence database limited to the proteins in the existing complex. To simulate a complex mixture scenario, we then included all proteins from the P. furiosus dataset in the sequence database; our strategy could quickly reproduce the results using the simplified database when a competing tool, Cross-Work, failed to do so. As such SIM-XL will be recommended for dealing with the studies of protein-structure and protein-protein-interaction in either simple or complex protein mixtures. It has a desktop graphic user interface but is also being designed for cloud computing. SIM-XL is integrated into the PatternLab for proteomics environment which offers a wide range of tools for downstream analysis for quantitative proteomics. 5º Congresso BrMass – 7 a 11 de Dezembro de 2013