AMEZIST

Overview

AMEZIST is an integrated analysis and reporting platform for biochemical research. It helps researchers understand what structural types of metabolites are detected, how they are distributed across chemical space, and how they may function within biological systems.

AMEZIST supports the full workflow from metabolite structural interpretation to chemical-space classification, biological interpretation, visualization, and PowerPoint / Excel report generation within a single local GUI environment.

Built on the design philosophy of “One Click．One Function．One Result．”, AMEZIST inherits and expands the BCC workflow for experimental planning, data analysis, and presentation preparation, enabling immediate deployment in research environments with minimal training cost.

A distinctive strength of AMEZIST is the integration of compound structural analysis with SIC / Extend-SIC (ESIC), an original method for analyzing the structural repertoire and chemical-space distribution of interpreted compounds.

Integrated Metabolite Analysis Workflow

AMEZIST is designed to answer three central questions in metabolomics and biochemical research:

1. What metabolites were detected?
   Structural interpretation of detected metabolites based on MS and MS/MS data.
2. How are the metabolites distributed and classified?
   Chemical-space analysis and classification of the detected compound repertoire using SIC / ESIC.
3. What is their biological significance?
   Interpretation of possible biological mechanisms, activities, and functional implications.

By connecting these steps with visualization and report generation, AMEZIST turns analytical results into presentation-ready materials for discussion, documentation, and research planning.

Scientific Foundations

Structural Isomer Cumulative molecular fingerprint (SIC)
Published in Communications Chemistry (Springer Nature)

The SIC method quantifies relative structural distances among isomers and visualizes their distribution in chemical space. It captures positional, skeletal, and functional-group isomerism—relationships difficult to resolve using conventional molecular descriptors.

In AMEZIST, SIC is extended and optimized as Extend-SIC (ESIC), enabling high-speed local analysis even for large-scale datasets.

BioChemCalc (BCC)
Published in Results in Engineering (Elsevier)

BCC provides one-click execution for Mass informatics (LC/MS analysis), chemoinformatics, bioinformatics, and statistical processing. Its design philosophy forms the foundation of AMEZIST.

AMEZIST redesigns these modules as a full superset, enabling high-capacity processing and workflow integration beyond the capabilities of the web version.

Features

1. High-speed local computation (fully offline)

All processing is executed locally, ensuring fast and secure computation without sending research data to external servers. It operates under restricted academic networks and handles large datasets reliably.

2. Complete superset of BCC

AMEZIST inherits BCC’s “one click, one function” design while expanding computational power, usability, and throughput. Existing workflows can be transferred with minimal training.

3. Extend-SIC (ESIC) for advanced chemical-space analysis

ESIC enables real-time analysis of large isomer libraries and quantitative comparison of structural relationships in chemical space.

4. Integrated research workflow

AMEZIST connects metabolite structural analysis, chemical-space and repertoire analysis, biological interpretation, visualization, log generation, and PowerPoint / Excel report creation within a single GUI, streamlining research from analysis to presentation.

5. Multi-domain support

• Mass informatics: Fragmentation and spectral analysis, MS spectral export to PPT, and others.
• Chemoinformatics: ESIC calculator and viewer, positional-isomer grouping, and others.
• Bioinformatics: Batch PCA, t-SNE, and UMAP analyses with PPT/Excel export, statistical analyses, and others.

6. High-quality PowerPoint / Excel outputs

AMEZIST produces polished figures, logs, and computed results suitable for conference presentations and manuscript preparation.

Capabilities

AMEZIST is a local integrated analysis platform for biologists and biochemical researchers that consolidates metabolite structural analysis, chemoinformatics, bioinformatics, visualization, and report generation into a single, unified GUI environment.

AMEZIST is composed of the following three modules:

• Mass Informatics
• Chemoinformatics
• Bioinformatics

The following functions are included in AMEZIST ver. 1.0.0.

Mass Informatics (Spectral interpretation and visualization)

• MS Matcher & PPT Expo: Generation of PPT-format graphs of MS spectra mirror plots and cos similarity.
• MS Fragment & PPT Expo: Fragment assignment in MS/MS spectra and generation of PPT-format graphs.
• Structure Annotation & PPT Expo: Molecular formula and structural analysis for MS1/MS2 data in mzML format, and generation of PPT-format graphs.

Chemoinformatics (Quantification of chemical space)

• Exact Mass Calculator: Exact mass calculation from molecular formulas and SMILES notation, detection of notation errors, and Excel output.
• ESIC Calculator & Viewer: ESIC calculation and visualization (viewer display), and Excel output.
• ESIC Positional Isomer Grouper: Grouping of positional isomers based on ESIC and Excel output.

Bioinformatics (Statistical analysis and visualization)

• Multivariate Analyzer-Bioinformatics: Batch execution of PCA, tSNE, and UMAP, and PPT/EXCEL output.
• Longevity Analyst: Calculation of the log-rank test and Kaplan–Meier (KM) analysis, and PPT output.
• Statistical Significance Tests: Batch calculation of the T-test, U-test, and Brunner–Munzel test, and Excel output.
• Volcano ploter: Generation of volcano plots using the results of the T-test, U-test, and Brunner–Munzel test, and Excel output.

Screenshots

Preview images of AMEZIST, including analysis panels, ESIC plots, and calculation tools.

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Case Studies

Institutional case studies will be published after formal adoption and approval.

Application Notes

Step-by-step technical notes and reproducible workflows will be published here.

Pricing (Region-specific, fixed amounts in JPY / USD / EUR)

• 1-user license: 200,000 JPY / 3,000 USD / 2,700 EUR
• 5-user license package: 700,000 JPY / 9,500 USD / 8,500 EUR
• 10-user license package: 1,200,000 JPY / 14,500 USD / 13,000 EUR
• 25-user license package: 2,800,000 JPY / 28,000 USD / 25,000 EUR
• 50-user license package: 5,500,000 JPY / 55,000 USD / 50,000 EUR
• 100-user license package: 10,000,000 JPY / 100,000 USD / 90,000 EUR

Licenses are provided on an annual basis.
A separate license is issued for each user.
Custom licensing options are available upon request.
Pricing is subject to change for future releases.

System Requirements

• Operating System: Windows 10 (64-bit) or later
• CPU: 64-bit multi-core processor
• Memory: 8 GB RAM (16 GB RAM recommended)
• Storage: 2 GB available disk space (SSD recommended)
• Display: Minimum resolution 1280 × 800 (Full HD recommended)
• Required Software: Microsoft PowerPoint (desktop) and Microsoft Excel (desktop)

A dedicated GPU is not required. Performance may vary depending on dataset size and analysis complexity.

Contact

For inquiries or implementation support:

Contact