Enzymatic protein digests do not assist in E. coli discrimination at the strain level using mass spectrometry

DOI: 10.5584/jiomics.v3i1.131

Authors

  • Ricardo J. Carreira Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
  • J.D. Nunes-Miranda Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
  • Alexandre Gonçalves Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
  • Gilberto Igrejas Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
  • Patrícia Poeta Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
  • Silvana Gómez-Meire SING Group, Informatics Department, Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain
  • Miguel Reboiro-Jato SING Group, Informatics Department, Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain
  • Florentino Fdez-Riverola SING Group, Informatics Department, Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain
  • Carlos Lodeiro REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
  • José Luís Capelo Martínez REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal

Abstract

Different procedures for matrix assisted laser desorption ionization time of flight mass spectrometry-based E. coli classification at the strain level using the enzymatic digestion of proteins from the cell lysate have been studied. The effects of ultrasonic energy as well as the effects of protein reduction and protein alkylation in the sample treatment and in the subsequent classification were assessed. The final optimal method for classification was then compared with an intact cell-based approach in a different set of samples. Our results show that E. coli classification at the strain level is possible as 12 different strains were correctly classified using intact cell analysis. The classification done using protein digestion does not classify the strains with the same level of confidence than intact cell analysis does. 

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Published

2021-02-22