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Toward Spectral Library-Free Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification
[Image: see text] Bacterial identification is of great importance in clinical diagnosis, environmental monitoring, and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interest and has bee...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989274/ https://www.ncbi.nlm.nih.gov/pubmed/29749232 http://dx.doi.org/10.1021/acs.jproteome.8b00065 |
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author | Cheng, Ding Qiao, Liang Horvatovich, Peter |
author_facet | Cheng, Ding Qiao, Liang Horvatovich, Peter |
author_sort | Cheng, Ding |
collection | PubMed |
description | [Image: see text] Bacterial identification is of great importance in clinical diagnosis, environmental monitoring, and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interest and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, that is, UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species, and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF. |
format | Online Article Text |
id | pubmed-5989274 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-59892742018-06-07 Toward Spectral Library-Free Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification Cheng, Ding Qiao, Liang Horvatovich, Peter J Proteome Res [Image: see text] Bacterial identification is of great importance in clinical diagnosis, environmental monitoring, and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interest and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, that is, UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species, and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF. American Chemical Society 2018-05-11 2018-06-01 /pmc/articles/PMC5989274/ /pubmed/29749232 http://dx.doi.org/10.1021/acs.jproteome.8b00065 Text en Copyright © 2018 American Chemical Society This is an open access article published under a Creative Commons Non-Commercial No Derivative Works (CC-BY-NC-ND) Attribution License (http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html) , which permits copying and redistribution of the article, and creation of adaptations, all for non-commercial purposes. |
spellingShingle | Cheng, Ding Qiao, Liang Horvatovich, Peter Toward Spectral Library-Free Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title | Toward Spectral
Library-Free Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title_full | Toward Spectral
Library-Free Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title_fullStr | Toward Spectral
Library-Free Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title_full_unstemmed | Toward Spectral
Library-Free Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title_short | Toward Spectral
Library-Free Matrix-Assisted Laser
Desorption/Ionization Time-of-Flight Mass Spectrometry Bacterial Identification |
title_sort | toward spectral
library-free matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry bacterial identification |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989274/ https://www.ncbi.nlm.nih.gov/pubmed/29749232 http://dx.doi.org/10.1021/acs.jproteome.8b00065 |
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