{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:58:37Z","timestamp":1761541117299},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Protein identification by mass spectrometry is commonly accomplished using a peptide sequence matching search algorithm, whose sensitivity varies inversely with the size of the sequence database and the number of post-translational modifications considered. We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved.<\/jats:p>\n               <jats:p>Availability: All data generated and the software are freely available for academic use at http:\/\/proteomics.fiocruz.br\/software\/sim.<\/jats:p>\n               <jats:p>Contact: \u00a0paulo@pcarvalho.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt106","type":"journal-article","created":{"date-parts":[[2013,2,28]],"date-time":"2013-02-28T20:37:14Z","timestamp":1362083834000},"page":"1343-1344","source":"Crossref","is-referenced-by-count":19,"title":["Effectively addressing complex proteomic search spaces with peptide spectrum matching"],"prefix":"10.1093","volume":"29","author":[{"given":"Diogo","family":"Borges","sequence":"first","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"},{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Yasset","family":"Perez-Riverol","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"},{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Fabio C. S.","family":"Nogueira","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Gilberto B.","family":"Domont","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Jesus","family":"Noda","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Felipe","family":"da Veiga Leprevost","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Vladimir","family":"Besada","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Felipe M. G.","family":"Fran\u00e7a","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Valmir C.","family":"Barbosa","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Aniel","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]},{"given":"Paulo C.","family":"Carvalho","sequence":"additional","affiliation":[{"name":"1 Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil, 2Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, 81350-010 Fiocruz, Paran\u00e1, Brazil, 3Department of Proteomics, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Cubanac\u00e1n, Playa, Ciudad de la Habana, Cuba, 4Proteomic Services, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 5Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2013,2,27]]},"reference":[{"key":"2023012810335094500_btt106-B1","doi-asserted-by":"crossref","first-page":"4105","DOI":"10.1002\/pmic.201100297","article-title":"Can the false-discovery rate be misleading?","volume":"11","author":"Barboza","year":"2011","journal-title":"Proteomics"},{"key":"2023012810335094500_btt106-B2","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/1471-2105-9-316","article-title":"PatternLab for proteomics: a tool for differential shotgun proteomics","volume":"9","author":"Carvalho","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012810335094500_btt106-B3","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1313s30","article-title":"Analyzing shotgun proteomic data with PatternLab for proteomics","author":"Carvalho","year":"2010","journal-title":"Curr. 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