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What Is PROTzilla?

PROTzilla is an open-source, browser-based tool for downstream proteomics mass spectrometry analysis.

It is designed to make proteomics data analysis more accessible, reproducible, and transparent. Instead of requiring users to write analysis scripts from scratch, PROTzilla provides workflow-based analysis steps for importing data, preprocessing datasets, performing statistical and exploratory analyses, integrating biological knowledge databases, and generating publication-ready plots.

PROTzilla is especially useful for researchers who want to analyze proteomics data through a graphical interface while still keeping their workflows structured, shareable, and reproducible.

What Is PROTzilla For?

PROTzilla helps users to:

• import proteomics data and metadata,
• preprocess and transform datasets,
• perform downstream data analysis,
• create visualizations for interpretation and reporting,
• integrate external biological knowledge databases,
• build reproducible workflows that can be shared and reused.

Where Should I Start?

This wiki is organized into three main sections:

• User Guide: for learning how to use PROTzilla in practice.
• Step Documentation: for understanding the available workflow steps.
• Developer Guide: for contributors and developers who want to understand or extend the codebase.