Explainer · Plain-language

What is a protocol paper?

A protocol paper is a peer-reviewed, citable article that describes the complete methods of a planned study before any results are collected. By making the design publicly available in advance, protocol papers promote transparency, enable scrutiny of methods, and strengthen confidence in eventual findings. They are common in clinical research, public health, and the social sciences.

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How protocol papers differ from preregistration

Preregistration and protocol papers both involve documenting a study's design in advance, but they serve different purposes and carry different weight. A preregistration entry — submitted to a registry such as PROSPERO or the Open Science Framework — is a time-stamped record of a study plan, typically reviewed only for completeness rather than scientific merit. A protocol paper, by contrast, undergoes independent peer review at a journal: reviewers assess whether the research question is justified, whether the design is appropriate, and whether the statistical plan is sound. This peer-reviewed status gives protocol papers greater credibility and means they function as standalone scholarly outputs. Researchers may do both: preregister with PROSPERO and then publish a protocol paper to provide a fuller, citable account of their methods. PROSPERO itself accepts systematic reviews, rapid reviews, and umbrella reviews, but does not accept scoping reviews.

The SPIRIT checklist

The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist provides evidence-based guidance on the minimum content that a clinical trial protocol should contain. First published in 2013 simultaneously in the BMJ and the Annals of Internal Medicine, SPIRIT listed 33 recommended items covering administrative information, introduction, methods, ethics, and dissemination plans. The checklist was updated in 2025 — the SPIRIT 2025 statement was published simultaneously across the BMJ, JAMA, The Lancet, Nature Medicine, and PLoS Medicine — reflecting advances in trial design, reporting, and regulatory requirements. SPIRIT is endorsed by the EQUATOR Network (Enhancing the QUAlity and Transparency Of health Research), the global body that coordinates reporting guidelines for health research, and is widely required by journals and ethics boards for clinical trial protocols.

Where protocol papers are published

Several journals specialise in publishing study protocols without requiring results. BMJ Open operates as a broad-scope open access journal that routinely publishes protocols for clinical trials, observational studies, and qualitative projects. Trials, published by BioMed Central, focuses on clinical trials at all stages and explicitly welcomes protocol papers as a recognised article type. JMIR Research Protocols, from JMIR Publications, covers digital health, health informatics, and related biomedical fields, and publishes protocols alongside pilot and feasibility reports. These journals apply full peer review to protocols and assign citable DOIs, meaning a protocol paper contributes to a researcher's publication record and can be referenced by other teams. For systematic review protocols specifically, PROSPERO — run by the Centre for Reviews and Dissemination at the University of York and funded by the National Institute for Health and Care Research (NIHR) — provides a dedicated international registry.

Benefits for transparency and replication

Publishing a study protocol in advance provides a public record that can be compared with the eventual results paper, making it straightforward to identify whether outcomes were changed, analyses were added post hoc, or primary endpoints were quietly demoted. This guards against outcome-reporting bias — a well-documented problem in which statistically significant or favourable findings are more likely to be published than null or negative ones. Protocol papers also benefit the broader research community: other groups working on similar questions can avoid duplication, can coordinate their work with the documented study, or can identify opportunities for collaboration. For researchers using the SPIRIT checklist, the process of completing all 33 items often reveals gaps or ambiguities in the design that can be resolved before data collection begins, improving the ultimate quality of the study.

Key facts

At a glance

Definition: A peer-reviewed journal article describing a study's methods before results are known
Peer review: Covers the scientific rationale and design, not merely completeness
Key checklist: SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials)
Current version: SPIRIT 2025, published in BMJ, JAMA, Lancet, Nature Medicine, PLoS Medicine
PROSPERO: Systematic review registry at University of York, funded by NIHR; does not accept scoping reviews
Key journals: BMJ Open, Trials (BioMed Central), JMIR Research Protocols

Common misconceptions

What people often get wrong

Often heard: A protocol paper is just a preregistration entry.

Actually: A protocol paper undergoes full peer review at a journal; a preregistration entry is typically reviewed only for completeness. They serve complementary purposes and researchers often do both.

Often heard: You cannot publish a protocol paper if results are already available.

Actually: Most journals require protocol papers to be submitted before data collection is complete, but some allow submission up until the point of data analysis — the key criterion is that results are not yet known.

Often heard: Protocol papers can only be published for clinical trials.

Actually: Journals such as BMJ Open and JMIR Research Protocols publish protocols for observational, qualitative, and mixed-methods studies as well as trials. PROSPERO accepts systematic review protocols across health and social care.

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