Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways
Glycans present extraordinary structural diversity commensurate with their involvement in numerous fundamental cellular processes including growth, differentiation, and morphogenesis. Unlike linear DNA and protein sequences, glycans have heterogeneous structures that differ in composition, branching...
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| Format: | Article |
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MDPI AG
2020-09-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/10/10/1383 |
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| author | Nobuaki Miura Hisatoshi Hanamatsu Ikuko Yokota Kazue Okada Jun-Ichi Furukawa Yasuro Shinohara |
| author_facet | Nobuaki Miura Hisatoshi Hanamatsu Ikuko Yokota Kazue Okada Jun-Ichi Furukawa Yasuro Shinohara |
| author_sort | Nobuaki Miura |
| collection | DOAJ |
| description | Glycans present extraordinary structural diversity commensurate with their involvement in numerous fundamental cellular processes including growth, differentiation, and morphogenesis. Unlike linear DNA and protein sequences, glycans have heterogeneous structures that differ in composition, branching, linkage, and anomericity. These differences pose a challenge to developing useful software for glycomic analysis. To overcome this problem, we developed the novel Toolbox Accelerating Glycomics (TAG) program. TAG consists of three units: ‘TAG List’ creates a glycan list that is used for database searching in TAG Expression; ‘TAG Expression’ automatically annotates and quantifies glycan signals and draws graphs; and ‘TAG Pathway’ maps the obtained expression information to biosynthetic pathways. Herein, we discuss the concepts, outline the TAG process, and demonstrate its potential using glycomic expression profile data from Chinese hamster ovary (CHO) cells and mutants lacking a functional <i>Npc1</i> gene (<i>Npc1</i> knockout (KO) CHO cells). TAG not only drastically reduced the amount of time and labor needed for glycomic analysis but also detected and quantified more glycans than manual analysis. Although this study was limited to the analysis of <i>N</i>-glycans and free oligosaccharides, the glycomic platform will be expanded to facilitate the analysis of <i>O</i>-glycans and glycans of glycosphingolipids. |
| first_indexed | 2024-03-10T15:59:22Z |
| format | Article |
| id | doaj.art-fc5114309a2240d8965f00b7e971252c |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T15:59:22Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-fc5114309a2240d8965f00b7e971252c2023-11-20T15:26:50ZengMDPI AGBiomolecules2218-273X2020-09-011010138310.3390/biom10101383Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic PathwaysNobuaki Miura0Hisatoshi Hanamatsu1Ikuko Yokota2Kazue Okada3Jun-Ichi Furukawa4Yasuro Shinohara5Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, JapanDepartment of Advanced Clinical Glycobiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita21, Nishi11, Kita-ku, Sapporo 001-0021, JapanDepartment of Advanced Clinical Glycobiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita21, Nishi11, Kita-ku, Sapporo 001-0021, JapanDepartment of Advanced Clinical Glycobiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita21, Nishi11, Kita-ku, Sapporo 001-0021, JapanDepartment of Advanced Clinical Glycobiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita21, Nishi11, Kita-ku, Sapporo 001-0021, JapanDepartment of Pharmacy, Kinjo Gakuin University, Nagoya 463-8521, JapanGlycans present extraordinary structural diversity commensurate with their involvement in numerous fundamental cellular processes including growth, differentiation, and morphogenesis. Unlike linear DNA and protein sequences, glycans have heterogeneous structures that differ in composition, branching, linkage, and anomericity. These differences pose a challenge to developing useful software for glycomic analysis. To overcome this problem, we developed the novel Toolbox Accelerating Glycomics (TAG) program. TAG consists of three units: ‘TAG List’ creates a glycan list that is used for database searching in TAG Expression; ‘TAG Expression’ automatically annotates and quantifies glycan signals and draws graphs; and ‘TAG Pathway’ maps the obtained expression information to biosynthetic pathways. Herein, we discuss the concepts, outline the TAG process, and demonstrate its potential using glycomic expression profile data from Chinese hamster ovary (CHO) cells and mutants lacking a functional <i>Npc1</i> gene (<i>Npc1</i> knockout (KO) CHO cells). TAG not only drastically reduced the amount of time and labor needed for glycomic analysis but also detected and quantified more glycans than manual analysis. Although this study was limited to the analysis of <i>N</i>-glycans and free oligosaccharides, the glycomic platform will be expanded to facilitate the analysis of <i>O</i>-glycans and glycans of glycosphingolipids.https://www.mdpi.com/2218-273X/10/10/1383glycomicsautomated annotationMALDI-TOF MSbiosynthetic pathwaysglycan diversityinformatics |
| spellingShingle | Nobuaki Miura Hisatoshi Hanamatsu Ikuko Yokota Kazue Okada Jun-Ichi Furukawa Yasuro Shinohara Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways Biomolecules glycomics automated annotation MALDI-TOF MS biosynthetic pathways glycan diversity informatics |
| title | Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways |
| title_full | Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways |
| title_fullStr | Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways |
| title_full_unstemmed | Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways |
| title_short | Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways |
| title_sort | toolbox accelerating glycomics tag glycan annotation from maldi tof ms spectra and mapping expression variation to biosynthetic pathways |
| topic | glycomics automated annotation MALDI-TOF MS biosynthetic pathways glycan diversity informatics |
| url | https://www.mdpi.com/2218-273X/10/10/1383 |
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