Examples
Worked examples
- Is an instance
A published PRISMA-P systematic-review protocol registered in PROSPERO before searches began
Counter-examples
Looks similar, but isn't
- Not an instance
A methods section of a results paper is not a protocol paper (it is a section of a different publication type)
Editorial commentary
A protocol paper is a peer-reviewed publication that fully describes the methodology of one specific, planned or ongoing research study — a clinical trial, systematic review, cohort study, or laboratory protocol — prior to or alongside execution, in enough detail to enable replication and to fix the study’s methods against undisclosed post-hoc revision. Its defining feature is scope: a protocol paper documents the plan for a single study, not a generalisable method other researchers would adopt across different studies.
Where protocol papers are published
Dedicated venues exist specifically for this format — BMJ Open, Trials, and Systematic Reviews are established examples — reflecting that publishing a study’s protocol is treated as a citable, first-class contribution distinct from the eventual results paper. Systematic-review protocols are commonly registered in PROSPERO in addition to, or instead of, standalone journal publication; clinical-trial protocols are commonly registered on ClinicalTrials.gov alongside any published protocol paper.
How this differs from adjacent publication types
- Versus a methods paper. A methods paper’s contribution is the method itself — a new or refined analytic technique, instrument, or computational approach intended for other researchers to adopt across their own, different studies. A protocol paper’s contribution is the pre-specified plan for one particular study; the methods it describes may be entirely standard, and its value lies in fixing them in advance for that specific study, not in the methods being novel.
- Versus a working paper. A working paper is research circulated in progress through an institutional series, at any stage of completeness, without the pre-registration function a protocol paper serves — it is not tied to a formal commitment to a pre-specified plan.
- Versus a Registered Report / Stage 1 protocol. A Registered Report’s Stage 1 protocol is peer-reviewed specifically for in-principle acceptance by a participating journal, with the journal committing in advance to publish the eventual Stage 2 results paper regardless of outcome. A protocol paper can exist entirely independently of the Registered Reports mechanism — published in a dedicated protocol-focused journal with no linked in-principle-acceptance commitment from the venue that will eventually publish the results.
- Versus a methods section. A methods section embedded within a results paper is not a protocol paper — it is a section of a different publication type, written after the fact and not independently peer-reviewed or citable as its own record.
Why researchers publish protocols separately
Publishing the protocol ahead of or alongside execution serves the same core purpose pre-registration generally serves: it commits the research team publicly to a specific design and analysis plan before outcomes are known, making later deviations visible and reducing the scope for undisclosed post-hoc changes to methods or endpoints that would otherwise be invisible to readers of the eventual results paper.
References
- Center for Open Science, Registered Reports initiative, cos.io/initiatives/registered-reports.
Also known as
Study protocol publication · Method protocol paper
Machine-readable encodings
Use in your systems
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