Criteria for Success
A successful Methods section:
- provides the reasons for choosing your methodology
- allows readers to confirm your findings through replication
Structure
Compare Authentic Annotated Examples for Methods and Results: note the correspondence of subheadings between the two sections.
Identify Your Purpose
The purpose of a Methods section is to describe how the questions/knowledge gap posed in the Introduction was answered in the Results section. Not all readers will be interested in this information. For those who are, the Methods section has two purposes:
1. Allow readers to judge whether the results and conclusions of the study are valid.
The interpretation of your results depends on the methods you used to obtain them. A reader who is skeptical of your results will read your Methods section to see if they can be trusted. They’ll want to know that you chose the most appropriate methods and performed the necessary controls. Without this content, skeptical readers might think your data and any conclusions drawn from them are unreliable.
2. Allow readers to repeat the study.
For readers interested in replicating your study, the Methods section should provide enough information for them to obtain the same or similar results.
Analyze your audience
Typically, only readers in your field will want to replicate your study or have the knowledge to assess your methodology. More general audiences will read the Introduction and then proceed straight to the Results. You can therefore assume that people reading your Methods understand methodologies that are frequently used in your field. To gauge the level of detail necessary for a given method, you can look at articles previously published in your target journal.
If your paper is designed to appeal to experts in more than one field, you still need to write your Methods for a single set of experts. For example, say you applied a novel computational approach to gain new insight into a well-characterized biological system. Is your goal to get to show biologists the value of your computational tool or to show computational scientists how they can help study biology? In the former case, assume less computational expertise: provide more extensive explanations for how methods work and why they were chosen.
Skills
Structure your methods according to experimental outputs
Methods describe the key intermediate outputs of your methodology and how you generated them, instead of providing a step-by-step protocol. For example, methods for microscopy sample preparation describe how to generate an imaging-ready sample, with fixed samples and permeabilized samples as possible intermediate outputs. With methods structured around the outputs of each step, your reader can easily connect how each step relates to the next, identify the purpose of each step, and assess whether alternative approaches might be more appropriate for producing a given output.
To write your methods section, decompose your methodology into a series of outputs. For each output, include key information, like how each output was treated to produce the next, reasons for choosing that methodology, and details needed for replication. Each sentence of your methods section will typically correspond to one output, even if multiple protocol steps are required to produce that output. If the outputs of each step are similar to each other, you may choose to consolidate these steps into a single sentence. For example, you might describe how your cells were fixed, permeabilized, and blocked in a single sentence.
The table below contains an example of how you might write a methods section for flow sorting experiments. In each row, we list the input, action, output, and optionally, why the step was performed. These elements are combined to form a single sentence in your methods section. Phrases in parentheses are additional technical details.
| Protocol | Input | Action | Why | Output | Methods |
| Grow cells overnight. | Cells | cultured | Cells at exponential phase | Cells were cultured (under X conditions) until exponential phase. | |
| Add ligand. | Cells at exponential phase | incubated with ligand | Ligand-treated cells | Cells at exponential phase were incubated in ligand (at X concentration). | |
| Wash. | Ligand-treated cells | washed | to minimize non-specific binding | Washed cell suspension | After incubation, cells were washed (with X buffer) to minimize non-specific binding. |
| Flow sort. | Washed cell suspension | sorted | to isolate strong binders | Strong binders | Washed cells were sorted (using X equipment) to isolate strong binders. |
Use sentence order to emphasize key aspects of each step
Introduce aspects of each step in order of their importance. Make sure to introduce the input of each methodological step before describing the exact reagents, software, or equipment used.
Samples were denatured in Laemmli buffer containing beta-mercaptoethanol.
not
4X Laemmli buffer and beta-mercaptoethanol were added to sample to obtain a final concentration of 1X Laemmli buffer and beta-mercaptoethanol.
You can also use sentence order to emphasize details that could affect experimental results. In the first sentence, the sentence order emphasizes the importance of avoiding cell lysis; in the second, removal of the supernatant is emphasized.
“Without lysing, cells were pelleted gently in order to remove supernatant.”
vs.
“In order to remove supernatant, cells were pelleted gently without lysing cells.”
vs.
“Cells were pelleted gently in order to remove supernatant without lysing cells.”
Use subheadings to organize content
As recommended for your Results section, use subheadings within your Methods to group related experiments and establish a logical flow. Write your Results section first, and then follow the order of Results subheadings when writing your Methods. The parallel structure will make it easy for readers to locate corresponding information in the two sections.
Subheadings for Methods and Results may not exactly correspond. Sometimes you may need multiple Methods subheadings to explain one Results subheading. Other times one Method subheading is enough to explain multiple Result subheadings.
Provide minimal essential detail
Provide only those details necessary for a reader to replicate the experiments presented in your study; anything more is extraneous. Remember that readers use Methods to help them assess the validity of your conclusions – do specify any methodological details that might cause someone to reach a different conclusion.
You can cite papers for standard methods, but any modifications or alterations should be clearly stated. When citing methods, cite the original paper in which a method was described instead of a paper that used the method. This helps avoid chains of citations that your reader must follow to find information about the method.
Avoid “we did…” or “the authors did…”
The Methods section should focus on the experiments, not the authors. Avoid phrasing your experiments as “We/The authors did ___”, even if it requires you to write in the passive voice.
“Samples were processed with standard DNA extraction protocols.”
not
“We processed the samples with standard DNA extraction protocols.”
This article was first published in 2016 and was written by Manu Kumar, Scott Olesen, and Diana Chien. It was updated in July 2021 by Cal Gunnarsson and Chris Doering.
Resources and Annotated Examples
Annotated Example 1
Zetsche et al., "Cpf1 is a single RNA-guided endonuclease...", Cell2015. Compare to the annotated examples in the Results section. 2 MB