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User Guide: Using the Deep Research Protocol
Generate comprehensive reference reports with Deep Research Comprehensive Reference Report Generation protocol - a flexible knowledge artifact for scripts, presentations, and collaboration.
User Guide: Using the Deep Research Protocol
This guide explains how to use ChatGPT Deep Research to generate a comprehensive reference report with the Step 1 protocol. The report is a knowledge-rich artifact you can use in many ways — as the foundation for scripts, presentations, or further collaboration.
Preparing Your Materials
Your Main Question or Topic
Prepare a clear question or topic for research, such as "What are the applications of graph databases in biomedical research?"
Optional Files
Upload one or more documents (such as research papers, notes, or reports).

Tip: Uploading multiple papers together gives ChatGPT stronger context for the report.
Choosing Which ChatGPT Level to Use
Standard Model
Quick, simple answers.
Thinking Model
Adds reasoning depth, good for exploratory work.
Pro Model
Creates a strong first draft of a Step 1 report.
Deep Research
The intended level for this protocol; best for a thorough, evidence-based report.

Recommendation: Use Pro for fast drafts. Use Deep Research when accuracy, citations, and comprehensiveness are essential.
Uploading Files
Open ChatGPT
Launch the ChatGPT interface in your browser
Click the paperclip (📎) icon
Find the upload button in the interface
Upload files
Upload one or more reference papers or documents
Prompting ChatGPT
After uploading files, ask ChatGPT to begin Step 1. A good starting prompt is:
Please use the Deep Research protocol to generate a comprehensive reference report on [your topic].
Example:

Please use the Deep Research protocol to generate a comprehensive reference report on the role of transformers in drug discovery. I have uploaded three recent papers to use as references.
What the Report Will Include
The Step 1 report is a structured Markdown document with:
Introduction and background
Key terms and definitions
Detailed explanations
(how and why)
Comparisons and alternatives
Use cases and examples
Limitations or challenges
Citations and supporting evidence
How to Use the Report
Once generated, the report becomes a flexible working resource. You can:
1
Proceed to Step 2 (Episode Planning)
Copy the report into a new chat and prompt ChatGPT:
Please use the Step 2 Episode Planning protocol to create an episode breakdown from this report.
2
Collaborate further
Open a new chat, upload the Step 1 report, and work with GPT-5 Pro or Deep Research to:
  • Expand or refine sections
  • Add new sources or citations
  • Reframe the material for a presentation, blog, or white paper
  • Generate scripts or summaries directly
The Step 1 report is not a dead end — it's a knowledge artifact you can reuse, improve, or transform for many different tasks.
Reviewing and Refining
Ensure your original question is fully answered.
Check that citations are present and clear.
Ask for expansions or updates if needed ("Expand the section on limitations with recent studies").
Edit the protocol. You can ask GPT-5-pro or Deep Research to help you tailor the protocol for your needs.
Ready to Start
✅ You're ready to start
Upload your question, provide supporting papers, select your model level (Pro or Deep Research recommended), and run the protocol. Then reuse the report in whichever direction your project requires.