Cargando…

Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize vari...

Descripción completa

Detalles Bibliográficos
Autores principales: Jia, Rui Zong, Zhang, Rong Juan, Wei, Qing, Chen, Wen Feng, Cho, Il Kyu, Chen, Wen Xin, Li, Qing X
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616259/
https://www.ncbi.nlm.nih.gov/pubmed/26500417
http://dx.doi.org/10.4172/jpb.1000357
_version_ 1782396593021911040
author Jia, Rui Zong
Zhang, Rong Juan
Wei, Qing
Chen, Wen Feng
Cho, Il Kyu
Chen, Wen Xin
Li, Qing X
author_facet Jia, Rui Zong
Zhang, Rong Juan
Wei, Qing
Chen, Wen Feng
Cho, Il Kyu
Chen, Wen Xin
Li, Qing X
author_sort Jia, Rui Zong
collection PubMed
description Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.
format Online
Article
Text
id pubmed-4616259
institution National Center for Biotechnology Information
language English
publishDate 2015
record_format MEDLINE/PubMed
spelling pubmed-46162592015-10-23 Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry Jia, Rui Zong Zhang, Rong Juan Wei, Qing Chen, Wen Feng Cho, Il Kyu Chen, Wen Xin Li, Qing X J Proteomics Bioinform Article Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour. 2015-05-31 2015 /pmc/articles/PMC4616259/ /pubmed/26500417 http://dx.doi.org/10.4172/jpb.1000357 Text en http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Article
Jia, Rui Zong
Zhang, Rong Juan
Wei, Qing
Chen, Wen Feng
Cho, Il Kyu
Chen, Wen Xin
Li, Qing X
Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title_full Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title_fullStr Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title_full_unstemmed Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title_short Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
title_sort identification and classification of rhizobia by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616259/
https://www.ncbi.nlm.nih.gov/pubmed/26500417
http://dx.doi.org/10.4172/jpb.1000357
work_keys_str_mv AT jiaruizong identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT zhangrongjuan identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT weiqing identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT chenwenfeng identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT choilkyu identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT chenwenxin identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry
AT liqingx identificationandclassificationofrhizobiabymatrixassistedlaserdesorptionionizationtimeofflightmassspectrometry