What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characteri...
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MDPI AG
2021-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/6/1243 |
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| author | Itaru Dekio Yuki Sugiura Susumu Hamada-Tsutsumi Yoshiyuki Murakami Hiroto Tamura Makoto Suematsu |
| author_facet | Itaru Dekio Yuki Sugiura Susumu Hamada-Tsutsumi Yoshiyuki Murakami Hiroto Tamura Makoto Suematsu |
| author_sort | Itaru Dekio |
| collection | DOAJ |
| description | Matrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characterized. In order to deepen the understanding of these peaks and to develop a more reasonable identification workflow, we applied proteogenomic approaches to assign the high-intensity peaks of MALDI–TOF spectra of two bacterial genera. First, the 3–22 kD proteomes of 5 <i>Cutibacterium</i> strains were profiled by UPLC–MS/MS, and the amino acid sequences were refined by referring to their genome in the public database. Then, the sequences were converted to <i>m</i>/<i>z</i> (<i>x</i>-axis) values based on their molecular masses. When the interspecies comparison of calculated <i>m</i>/<i>z</i> values was well-fitted to the observed peaks, the peak assignments for the five <i>Cutibacterium</i> species were confirmed. Second, the peak assignments for six <i>Staphylococcus</i> species were performed by using the above result for <i>Cutibacterium</i> and referring to ribosomal subunit proteins coded on the <i>S10-spc-alpha</i> operon (the <i>S10</i>-GERMS method), a previous proteomics report by Becher et al., and comprehensive genome analysis. We successfully assigned 13 out of 15 peaks for the <i>Cutibacterium</i> species and 11 out of 13 peaks for the <i>Staphylococcus</i> species. DNA-binding protein HU, the CsbD-like protein, and 50S ribosomal protein L7/L12 were observed in common. The commonality suggests they consist of high-intensity peaks in the MALDI spectra of other bacterial species. Our workflow may lead to the development of a more accurate species identification database of MALDI–TOF mass spectrometry based on genome data. |
| first_indexed | 2024-03-10T10:36:47Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T10:36:47Z |
| publishDate | 2021-06-01 |
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| series | Microorganisms |
| spelling | doaj.art-19438ab54dc849ccacbe22fcf48eb35c2023-11-21T23:12:27ZengMDPI AGMicroorganisms2076-26072021-06-0196124310.3390/microorganisms9061243What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative ProteogenomicsItaru Dekio0Yuki Sugiura1Susumu Hamada-Tsutsumi2Yoshiyuki Murakami3Hiroto Tamura4Makoto Suematsu5Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, JapanDepartment of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, JapanDepartment of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, JapanSeikakai Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, JapanDepartment of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, JapanDepartment of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, JapanMatrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characterized. In order to deepen the understanding of these peaks and to develop a more reasonable identification workflow, we applied proteogenomic approaches to assign the high-intensity peaks of MALDI–TOF spectra of two bacterial genera. First, the 3–22 kD proteomes of 5 <i>Cutibacterium</i> strains were profiled by UPLC–MS/MS, and the amino acid sequences were refined by referring to their genome in the public database. Then, the sequences were converted to <i>m</i>/<i>z</i> (<i>x</i>-axis) values based on their molecular masses. When the interspecies comparison of calculated <i>m</i>/<i>z</i> values was well-fitted to the observed peaks, the peak assignments for the five <i>Cutibacterium</i> species were confirmed. Second, the peak assignments for six <i>Staphylococcus</i> species were performed by using the above result for <i>Cutibacterium</i> and referring to ribosomal subunit proteins coded on the <i>S10-spc-alpha</i> operon (the <i>S10</i>-GERMS method), a previous proteomics report by Becher et al., and comprehensive genome analysis. We successfully assigned 13 out of 15 peaks for the <i>Cutibacterium</i> species and 11 out of 13 peaks for the <i>Staphylococcus</i> species. DNA-binding protein HU, the CsbD-like protein, and 50S ribosomal protein L7/L12 were observed in common. The commonality suggests they consist of high-intensity peaks in the MALDI spectra of other bacterial species. Our workflow may lead to the development of a more accurate species identification database of MALDI–TOF mass spectrometry based on genome data.https://www.mdpi.com/2076-2607/9/6/1243<i>Cutibacterium</i><i>Staphylococcus</i>proteomicsMALDI–TOF mass spectrometryhigh-intensity peaks<i>S10</i>-GERMS |
| spellingShingle | Itaru Dekio Yuki Sugiura Susumu Hamada-Tsutsumi Yoshiyuki Murakami Hiroto Tamura Makoto Suematsu What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics Microorganisms <i>Cutibacterium</i> <i>Staphylococcus</i> proteomics MALDI–TOF mass spectrometry high-intensity peaks <i>S10</i>-GERMS |
| title | What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics |
| title_full | What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics |
| title_fullStr | What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics |
| title_full_unstemmed | What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics |
| title_short | What Do We See in Spectra?: Assignment of High-Intensity Peaks of <em>Cutibacterium</em> and <em>Staphylococcus</em> Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics |
| title_sort | what do we see in spectra assignment of high intensity peaks of em cutibacterium em and em staphylococcus em spectra of maldi tof mass spectrometry by interspecies comparative proteogenomics |
| topic | <i>Cutibacterium</i> <i>Staphylococcus</i> proteomics MALDI–TOF mass spectrometry high-intensity peaks <i>S10</i>-GERMS |
| url | https://www.mdpi.com/2076-2607/9/6/1243 |
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