核糖体峰：一种通过核糖体蛋白的 m/z 数据进行细菌分类的网络工具。

Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins.

机构信息

Postgraduate Program in Applied Computing, Department of Computer Science, State University of Ponta Grossa, PR, Brazil.

Microbial Molecular Biology Laboratory, Sector of Biological and Health Sciences, State University of Ponta Grossa, PR, Brazil.

出版信息

Bioinformatics. 2018 Sep 1;34(17):3058-3060. doi: 10.1093/bioinformatics/bty215.

DOI:10.1093/bioinformatics/bty215

PMID:29659702

Abstract

SUMMARY

MALDI-TOF MS is a rapid, sensitive and economic tool for bacterial identification. Highly abundant bacterial proteins are detected by this technique, including ribosomal proteins (r-protein), and the generated mass spectra are compared with a MALDI-TOF MS spectra database. Currently, it allows mainly the classification of clinical bacteria due to the limited number of environmental bacteria included in the spectra database. We present a wide-ranging bacterium classifier tool, called Ribopeaks, which was created based on r-protein data from the Genbank. The Ribopeaks database has more than 28 500 bacterial taxonomic records. It compares the incoming m/z data from MALDI-TOF MS analysis with models stored in the Ribopeaks database created by machine learning and then taxonomically classifies the bacteria.

AVAILABILITY AND IMPLEMENTATION

The software is available at http://www.ribopeaks.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）是一种快速、敏感且经济的细菌鉴定工具。该技术可检测到高度丰富的细菌蛋白，包括核糖体蛋白（r-protein），并将生成的质谱与 MALDI-TOF MS 质谱数据库进行比较。目前，由于质谱数据库中包含的环境细菌数量有限，它主要用于临床细菌的分类。我们介绍了一种广泛的细菌分类工具，称为 Ribopeaks，它是基于 Genbank 中的 r-protein 数据创建的。Ribopeaks 数据库包含超过 28500 个细菌分类记录。它将来自 MALDI-TOF MS 分析的传入 m/z 数据与通过机器学习在 Ribopeaks 数据库中创建的模型进行比较，然后对细菌进行分类。