The research protocol serves as your road map for initiating, conducting, and disseminating your research; It is comprised of the Introduction/Literature Review, the Methodology, and the References that support your proposed research project. 

The research protocol is initiated as a vehicle to present to the Institutional Review Board (IRB) in order to gain approval for your proposed research project.  After approval has been granted, the protocol serves as the foundation for your completed project manuscript to be submitted for publication.  The standard format for a research paper includes

• Introduction / Literature Review
• Methodology
• Results
• Conclusion
• References

Thus, the research protocol only lacks the results and conclusions that will come after data collection and data analysis.  Therefore, if the protocol has been written with care, the completed manuscript will only require the addition of the results and conclusions, in order to be ready for journal submission.