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Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids
Matrix-assisted laser desorption–ionization/time of flight mass spectrometry (MALDI-TOF MS) has been widely implemented for the rapid identification of microorganisms. Although most bacteria, yeasts and filamentous fungi can be accurately identified with this method, some closely related species sti...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711916/ https://www.ncbi.nlm.nih.gov/pubmed/33276478 http://dx.doi.org/10.3390/jof6040330 |
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author | Zvezdanova, Margarita E. Arroyo, Manuel J. Méndez, Gema Guinea, Jesús Mancera, Luis Muñoz, Patricia Rodríguez-Sánchez, Belén Escribano, Pilar |
author_facet | Zvezdanova, Margarita E. Arroyo, Manuel J. Méndez, Gema Guinea, Jesús Mancera, Luis Muñoz, Patricia Rodríguez-Sánchez, Belén Escribano, Pilar |
author_sort | Zvezdanova, Margarita E. |
collection | PubMed |
description | Matrix-assisted laser desorption–ionization/time of flight mass spectrometry (MALDI-TOF MS) has been widely implemented for the rapid identification of microorganisms. Although most bacteria, yeasts and filamentous fungi can be accurately identified with this method, some closely related species still represent a challenge for MALDI-TOF MS. In this study, two MALDI-TOF-based approaches were applied for discrimination at the species-level of isolates belonging to the Cryptococcus neoformans complex, previously characterized by Amplified Fragment Length Polymorphism (AFLP) and sequencing of the ITS1-5.8S-ITS2 region: (i) an expanded database was built with 26 isolates from the main Cryptococcus species found in our setting (C. neoformans, C. deneoformans and AFLP3 interspecies hybrids) and (ii) peak analysis and data modeling were applied to the protein spectra of the analyzed Cryptococcus isolates. The implementation of the in-house database did not allow for the discrimination of the interspecies hybrids. However, the performance of peak analysis with the application of supervised classifiers (partial least squares-discriminant analysis and support vector machine) in a two-step analysis allowed for the 96.95% and 96.55% correct discrimination of C. neoformans from the interspecies hybrids, respectively. In addition, PCA analysis prior to support vector machine (SVM) provided 98.45% correct discrimination of the three analyzed species in a one-step analysis. This novel method is cost-efficient, rapid and user-friendly. The procedure can also be automatized for an optimized implementation in the laboratory routine. |
format | Online Article Text |
id | pubmed-7711916 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-77119162020-12-04 Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids Zvezdanova, Margarita E. Arroyo, Manuel J. Méndez, Gema Guinea, Jesús Mancera, Luis Muñoz, Patricia Rodríguez-Sánchez, Belén Escribano, Pilar J Fungi (Basel) Article Matrix-assisted laser desorption–ionization/time of flight mass spectrometry (MALDI-TOF MS) has been widely implemented for the rapid identification of microorganisms. Although most bacteria, yeasts and filamentous fungi can be accurately identified with this method, some closely related species still represent a challenge for MALDI-TOF MS. In this study, two MALDI-TOF-based approaches were applied for discrimination at the species-level of isolates belonging to the Cryptococcus neoformans complex, previously characterized by Amplified Fragment Length Polymorphism (AFLP) and sequencing of the ITS1-5.8S-ITS2 region: (i) an expanded database was built with 26 isolates from the main Cryptococcus species found in our setting (C. neoformans, C. deneoformans and AFLP3 interspecies hybrids) and (ii) peak analysis and data modeling were applied to the protein spectra of the analyzed Cryptococcus isolates. The implementation of the in-house database did not allow for the discrimination of the interspecies hybrids. However, the performance of peak analysis with the application of supervised classifiers (partial least squares-discriminant analysis and support vector machine) in a two-step analysis allowed for the 96.95% and 96.55% correct discrimination of C. neoformans from the interspecies hybrids, respectively. In addition, PCA analysis prior to support vector machine (SVM) provided 98.45% correct discrimination of the three analyzed species in a one-step analysis. This novel method is cost-efficient, rapid and user-friendly. The procedure can also be automatized for an optimized implementation in the laboratory routine. MDPI 2020-12-02 /pmc/articles/PMC7711916/ /pubmed/33276478 http://dx.doi.org/10.3390/jof6040330 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zvezdanova, Margarita E. Arroyo, Manuel J. Méndez, Gema Guinea, Jesús Mancera, Luis Muñoz, Patricia Rodríguez-Sánchez, Belén Escribano, Pilar Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title | Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title_full | Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title_fullStr | Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title_full_unstemmed | Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title_short | Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids |
title_sort | implementation of maldi-tof mass spectrometry and peak analysis: application to the discrimination of cryptococcus neoformans species complex and their interspecies hybrids |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711916/ https://www.ncbi.nlm.nih.gov/pubmed/33276478 http://dx.doi.org/10.3390/jof6040330 |
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