The new Ribopeaks (RPK-II): Updated and enlarged tool for bacterial classification based on r-protein m/z data

Renann Rodrigues da Silva; Douglas Tomachewski; Laís Priscila Karas; Carolina Weigert Galvão; José Carlos Ferreira da Rocha; Edmar Miyoshi; Rafael Mazer Etto

doi:10.1016/j.jprot.2023.105008

The new Ribopeaks (RPK-II): Updated and enlarged tool for bacterial classification based on r-protein m/z data

J Proteomics. 2023 Oct 30:289:105008. doi: 10.1016/j.jprot.2023.105008. Epub 2023 Sep 28.

Authors

Renann Rodrigues da Silva¹, Douglas Tomachewski¹, Laís Priscila Karas², Carolina Weigert Galvão¹, José Carlos Ferreira da Rocha³, Edmar Miyoshi², Rafael Mazer Etto⁴

Affiliations

¹ Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil.
² Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Biomedical Sciences, State University of Ponta Grossa, Paraná, Brazil.
³ Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Applied Computing, State University of Ponta Grossa, Paraná, Brazil.
⁴ Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Applied Computing, State University of Ponta Grossa, Paraná, Brazil. Electronic address: mazeretto@uepg.br.

PMID: 37775078
DOI: 10.1016/j.jprot.2023.105008

Abstract

Ribopeaks is a rapid, sensitive, and economic web tool for bacterial identification based on m/z data from MALDI-TOF MS. To provide greater accuracy and robustness in the Ribopeaks analyzes we present an updated bacterial identification tool version, called Ribopeaks II (RPK-II). RPK-II contains a larger database, with r-protein data from fully sequenced bacterial genomes and optimized algorithms. Furthermore, this new version provides additional information about the identified bacterium, regarding antibiotic resistance.

Keywords: Antibiotic resistance; Bacterial identification; MALDI-TOF MS; Machine learning; Proteomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Bacteria*
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization