2.1.1 Study protocol

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​​​​​​​​​​​​​A. Background & Definitions

Within the EQIPD Quality System and the Toolbox, the term "study protocol" refers to a document that is used to describe and summarize information related to a specific study (experiment).

A single study protocol may contain references to one or more research methods and assays. For protocols for specific research protocols and assays, please refer to item 3.5.2 Protocols for methods and assays.

B. Guidance & Expectations

It is strongly recommended that, for every study (experiment), there is a study protocol prepared prior to the study being conducted.

Each study protocol should identify author(s), date when it was created and a unique ID of the study that it describes.

EQIPD has developed a template (please see below) that outlines the suggested structure and content of a study protocol.

This template is provided as a general guidance and serves only as an example:

  1. Title of the study
  2. Study hypothesis
  3. 2.1.4 Purpose of research
    1. ​Indicate whether the research is undertaken with the intention to inform a formal knowledge claim
  4. Choice of experimental model(s) or method(s)
    1. Describe how and why specific models and/or methods were chosen (e.g. based on 2.1.3 Appraisal of literature and systematic reviews
    2. If animal subjects are involved, justify why alternative are not suitable; as well as the selection of species, strain, age, and sex (if applicable)
  5. Choice of controls
    1. Describe the controls (negative, positive, shams), why and how these were chosen (e.g. based on 2.1.3 Appraisal of literature and systematic reviews
    2. If a positive control is included, indicate explicitly how the study outcome will be interpreted if positive control fails.
  6. Measures against risks of bias
    1. 2.1.8 Randomisation (if selected, a randomisation protocol must be available)
    2. 2.1.7 Blinding (if selected, a blinding protocol must be available)
    3. If randomization and/or blinding are not applied, please describe the reasons as well as any other measures to control the risks of bias that will be applied.
  7. Sample size
    1. Describe methods used to estimate the sample size (such as power analysis).
    2. For definitions and guidance see section 2.1.6 Sample size and power analysis
    3. Specify the primary outcome measure that was used to determine the sample size (see ARRIVE Essential - Outcome measures)
    4. The sample size is the number of experimental units per group (for definition of experimental unit – see ARRIVE Essential - Study design)
    5. Specify the exact number of experimental units allocated to each group, and the total number in each experiment.
    6. For definitions and guidance on sample size estimation and power analysis, please follow the link.
  8. Inclusion and exclusion criteria
    1. Indicate any 2.1.9 Inclusion and exclusion criteria to be applied
  9. Animal resources, reagents and materials
    1. Include a detailed description of reagents and materials and/or provide references to separate document(s) with the relevant information (e.g. use the description in 3.3.3 Management of research materials and reagents to add information to your Dossier)
    2. If animals are used, provide sufficient details expected for reporting (ARRIVE 2.0)
  10. Study design overview
    1. For complex study designs, include a visual representation that more easily interpreted than a text description (e.g. a timeline diagram, table or flow chart – e.g. using an Experimental Design Assistant).
  11. Experimental procedures
    1. Include a detailed description of methods and experimental procedures and/or provide references to separate document(s) with the relevant information (e.g. if you chose to use section 3.5.2 of the Dossier for storing 3.5.2 Protocols for methods and assays)
    2. If experimental methods are not described in separate documents, follow ARRIVE 2.0 Recommended Set suggestions (items 14-17 here as well as guidance provided here)
    3. If more than one method or procedure is used, describe sequence or experimental workflow
    4. For each experimental group, including controls, describe the procedures in enough detail to allow others to replicate them, including (more guidance - ARRIVE Essential - Experimental procedures)
      1. What was done, how it was done and what was used
      2. When and how often
      3. Where (including detail of any acclimation periods)
      4. Why (provide rationale for procedures)
  12. Data analysis
    1. Describe the processing of raw data (for definition of raw data – see section 2.3.1 Generation, recording, handling and archiving of raw data​)
    2. Describe statistical method(s) to be applied for each analysis (2.3.3 Statistical analysis)
    3. Describe any methods used to assess whether the data met the assumptions of the statistical approach (ARRIVE Essential - Statistical methods)
  13. Amendments
    1. Describe what was changed in the original study protocol, why, when and by whom
    2. When amending the study protocol, please make sure not to over-write the original version
    3. Amendments may be saved as documents separate from the original study protocol
  14. References
    1. If necessary, include references
  15. Preregistration
    1. ​EQIPD strongly recommends to pre-register study protocol (more information – 2.1.11 Preregistration)
    2. If pre-registered, please indicate the platform used, registration link and other relevant reference information


  • If study protocol references to other protocols or dociuments (e.g. protocol for a specific experimental method), is the reference made to the current (relevant) version)?

C. Resources

Template to create a study protocol based on the above guidance - 2.1.1 Study protocol.docx, 2.1.1 Study protocol with macro.docm

Experimental design tools:

  • MANILA (Matched Animal Analysis): link to the original article ([1]) and the tool ([2])
  • NC3Rs’ Experimental Design Assistant [3]

back to Toolbox

Next item: 2.1.2 Unique study ID