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A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.
Luo, Xiyang; Bittremieux, Wout; Griss, Johannes; Deutsch, Eric W; Sachsenberg, Timo; Levitsky, Lev I; Ivanov, Mark V; Bubis, Julia A; Gabriels, Ralf; Webel, Henry; Sanchez, Aniel; Bai, Mingze; Käll, Lukas; Perez-Riverol, Yasset.
Afiliación
  • Luo X; Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, 400065 Chongqing, China.
  • Bittremieux W; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States.
  • Griss J; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
  • Deutsch EW; Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria.
  • Sachsenberg T; Institute for Systems Biology (ISB), Seattle, Washington 98109, United States.
  • Levitsky LI; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany.
  • Ivanov MV; V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 142432, Russia.
  • Bubis JA; V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 142432, Russia.
  • Gabriels R; V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 142432, Russia.
  • Webel H; VIB-UGent Center for Medical Biotechnology, B-9052 Ghent, Belgium.
  • Sanchez A; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
  • Bai M; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark.
  • Käll L; Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 20502 Malmö, Sweden.
  • Perez-Riverol Y; Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, 400065 Chongqing, China.
J Proteome Res ; 21(6): 1566-1574, 2022 06 03.
Article en En | MEDLINE | ID: mdl-35549218
Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-cluster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica / Espectrometría de Masas en Tándem Tipo de estudio: Guideline Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2022 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteómica / Espectrometría de Masas en Tándem Tipo de estudio: Guideline Idioma: En Revista: J Proteome Res Asunto de la revista: BIOQUIMICA Año: 2022 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos