Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways
Abstract
:1. Introduction
2. Materials and Methods
2.1. Overview of Toolbox Accelerating Glycomics (TAG)
2.2. Implementation of TAG
2.2.1. Interface
2.2.2. TAG List
2.2.3. TAG Expression
2.2.4. TAG Pathway
2.3. Experimental Glycomic Analysis of N-glycans and FNGs for Npc1 KO CHO Cells
2.3.1. Extraction of Cellular Glycoproteins and Free Oligosaccharides
2.3.2. Glycoblotting Procedure and MALDI-TOF/TOF MS Analysis
3. Results and Discussion
3.1. Glycan Expression Analysis of Npc1 KO CHO Cells
3.2. Glycan Expression Variation Mapped to Biosynthetic Pathways
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Button Name | Function |
---|---|
TAG List | Generating a glycan list to be employed in TAG Expression. TAG List is a separate program written in the awk script language. |
TAG Expression | Glycan annotation, quantitation, statistical analysis, graphing. |
TAG Pathway (N-glycan) | Visualizing variation in N-glycan expression based on N-glycan biosynthetic pathways. |
TAG Pathway (FOS) | Visualizing variation in FNG expression based on FNG biosynthetic pathways. |
TAG Pathway (N-glycan + FOS) | Visualizing variation in both N-glycans and FNGs based on N-glycan and FNG biosynthetic pathways. |
Cell Position | Data Type | Data |
---|---|---|
A2 | Real number | Quantity of internal standard. |
B2 | Real number | Error tolerance for precursor m/z. |
C2 | Real number | Total quantity (µg) of protein. |
D2 | Integer | Number to distinguish experimental groups. For example, in the case of the current analysis (see text), wt(−) 1 is 1, NPC(−) is 2, and NPC(+) 1 is 3. |
E2 | Strings | Short name of the experiment. For example, in the case of the current analysis (see text), wt(−), NPC(−), and NPC(+) fall under this category. |
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Share and Cite
Miura, N.; Hanamatsu, H.; Yokota, I.; Okada, K.; Furukawa, J.-I.; Shinohara, Y. Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways. Biomolecules 2020, 10, 1383. https://0-doi-org.brum.beds.ac.uk/10.3390/biom10101383
Miura N, Hanamatsu H, Yokota I, Okada K, Furukawa J-I, Shinohara Y. Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways. Biomolecules. 2020; 10(10):1383. https://0-doi-org.brum.beds.ac.uk/10.3390/biom10101383
Chicago/Turabian StyleMiura, Nobuaki, Hisatoshi Hanamatsu, Ikuko Yokota, Kazue Okada, Jun-Ichi Furukawa, and Yasuro Shinohara. 2020. "Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways" Biomolecules 10, no. 10: 1383. https://0-doi-org.brum.beds.ac.uk/10.3390/biom10101383