Glycopeptide Composition Data Interpretation, Integration and Visualization
Demystifying Glycopeptide Composition Data Visualization through Advanced Tools
With the support of glycoinformatics, our well-trained team provides comprehensive Analysis/Prediction Services. Protein abundance and post-translational modifications in complex biological samples are important factors affecting glycopeptide identification. Glycopeptides have microscopic heterogeneity, and intact glycopeptide signals are more difficult to recognize than naked peptide signals. Glycan Data Interpretation, Integration and Visualization provide various computational tools for glycopeptide data visualization. Glycopeptides have multiple biological functions. To identify the corresponding function of a specific structure, CD BioGlyco provides reliable glycopeptide composition data interpretation, integration, and visualization.
Preprocessing
Our lab has a rich data repository and experienced library builders to help clients develop high-quality libraries and software. Peptide sequences processed by the software generate corresponding ion libraries. our lab supports clients to freely choose the retention time (RT) used for peptide(s) and precursor mass.
Based on the experimental data and glycopeptide characteristics provided by the client, we provide comprehensive glycopeptide computational biology information screening services.
General software setup
Our computationalists transform analytical data into functional modular tools and process them in a software pipeline of graphical editors. This strategy provides a superior analytical path for glycopeptide composition data interpretation, integration, and visualization.
We support manual annotation of fragment ion spectra and add new identification methods (de novo manual sequencing).
Data visualization
Feature detection: Our researchers analyze the correlation between fragment spectra and individual analytes through glycopeptide signatures and precursor positions. Moreover, we offer charge state and single isotope mass correction services.
Glycopeptide filtering: Our experienced computational team provides glycopeptide sorting services and spectral scoring calculation services based on peak intensities and peaks of all matched ions. To distinguish between spurious results, we evaluate spectral and glycopeptide properties using different color distributions.
Glycopeptide identification: Based on reliable data analysis, we provide all possible peptide sequences, peptide masses, glycosylation sites, a, b, c, and x, y, z ion sequences dependent on the number of missing cleavages, and fixed and variable modifications.
Publication
Technology: Data independent acquisition (DIA) MS, Data dependent acquisition (DDA) MS
Journal: Molecular Omics
Published: 2020
IF: 3.0
Results: In this study, the researchers developed a new strategy for the automated construction of peptide and glycopeptide DIA ion libraries. The strategy identifies and measures various N- and O-glycopeptide classes in glycoproteins. Moreover, it is also applicable to the analysis of glycopeptides in simple mixtures of yeast cell wall glycoproteome and mammalian glycoproteins. The strategy provides valuable value for glycopeptide data interpretation and visualisation.
Fig.1 DDA and DIA analysis of yeast glycopeptides. (Phung, et al., 2020)
Applications
- Glycopeptide composition data visualization can be used to efficiently identify common and rare glycoforms in glycopeptide-rich serum samples.
- Glycopeptide composition data visualization can be used for the identification of glycopeptides in complex biological samples.
- Glycopeptide composition data visualization can be used to detect global compositional glycosylation profiles of the glycoproteome.
Advantages of Us
- Our researchers pay extra attention to peptide forms produced by different charge states and modifications.
- We avoid spurious results by adjusting the necessary input node.
- Our lab provides validation at every step of the analysis of glycopeptide composition data visualization.
Frequently Asked Questions
- What is an intact glycopeptide?
- The strategy for intact glycopeptides is to fragment the intact glycopeptide without separating the sugar chain from the peptide. We use the electron transfer dissociation (ETD), where the sugar chain is not fragmented but the peptide is fragmented, and then combine it with the higher energy collisional dissociation (HCD) spectra for analysis.
- What are the commonly used tools for glycopeptide software setup?
- Using oxonium ion scoring scheme for glycopeptide fragment spectra filtering
- Collection of candidate glycopeptides by in silico digestion of protein sequences
- Precursor matching with possible glycan composition and peptide sequences
- An annotation tool for glycopeptide fragment ions
CD BioGlyco has computational glycobiologists who provide high-performance glycopeptide composition data interpretation, integration, and visualization. Our researchers accelerate our clients' progress in glycopeptide visualization studies with proven strategies. Please feel free to contact us.
Reference
- Phung, T.K.; et al. DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides. Molecular Omics. 2020, 16(2): 100-112.
For research use only. Not intended for any diagnostic use.
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