30 Materials & Methods
30.1 Key Insights
This is your chance to increase the reader’s confidence in your results by convincing them of your competence.
- What experiments did you perform to answer the central question
- How you did them, exactly?
Provide enough detail so that an experienced scientist can repeat the experiments and evaluate the validity of your approach.
30.2 Structure
Since this section serves as a stand-alone reference, arrange information in a clear and accessible format. Each Material or Method is described in its own sub-section.
Materials Each sub-section states what was used, how much was used, and where it came from. Materials include all consumables and instruments specific to your methods, e.g. drugs, reagents chemicals, instruments, media, buffers, gasses, plasmids, enzymes, among others, and all subjects examined, e.g. cell lines, species, population, patients, etc., including their quantity. If you do not describe the generation or collection of the samples, a reference to the origin must be included (person, company or laboratory and location).
Methods Each sub-section describes what was done in a thorough but concise manner. For standard techniques, the original paper is commonly cited. Include non-standard instrumentation settings, or changes to the standard protocol, that allowed you to obtain your data. Specialized software or complex statistical calculations, must also be described.
30.3 Writing Check-list
Use the following check list to determine if you’ve left out anything important
30.3.1 Sub-section Heading
- State the materials or method simply and clearly.
30.3.2 Preparation
- Were the samples systematically treated in some way?
- Where did they come from?
30.3.3 Indicators (Indirect measurement)
- Is the measured variable a ``proxy’’ of another variable that cannot be directly measured?
30.3.4 Statistics
- Which statistical tests were used?
- Which measurements were compared?
- How were different results normalized?
30.3.5 Standard Operating Procedures (SOPs)
- Has your laboratory published SOPs to standardize handling and downstream analysis?
30.4 Details
30.4.1 Modification of Standard Procedures
Many of the techniques used in your experiments will be standard laboratory practice. Often the laboratory that perfected the technique has published a method paper; this should be referenced. If you have made significant modifications to the protocol, they should be stated.
30.4.2 Presenting Data and Results
In the laboratory, the experimental design changes as results become available, making it tempting to explain why specific experiments were carried out. However, it is best to avoid this in the Methods section, restrict yourself to a pure description of the technique, rather than explaining the rationale for its choice.
30.4.3 Use Pre-existing Stock Phrases
Mostly every technique you describe in this section has been used in other laboratories. If you find it difficult to describe a specific technique, you will find stock phrases in the literature. This is acceptable re-use of language, rather than plagiarism, but note that this only applies to the Materials & Methods section.
```{example, name=“Examination of a Materials & Methods Section”}
The following excerpt from a Material & Methods section is from a paper reporting genetic copy number variation in a malarial parasite genome. Often the Materials and Methods section is the most poorly written section of a paper, probably because it is the least read. Consider these sentence templates and how this example fulfills the purpose of a Materials & Methods section.
Heading: … culture, gDNA Preparation and Strain Identification.
Paragraph 1: Source of Material
- … lines were obtained either from … repository or were kindly provided by … (… ). (Source of material)
- … culture in erythrocytes was performed using standard methods (42), and genomic DNA (gDNA) was extracted using the … kit (
) and eluted into a … buffer. (Reference for standard method, sources, unique parameters)
Paragraph 2: Classification Analysis of Material
- Genomic DNA from … was first examined by sequencing the … as a check for identity. (Standard technique. Confirmation)
- Two pairs of cultured lines (… and … ) had identical sequences at … , and subsequent sequencing showed each pair was identical at … other polymorphic genes. (Data)
- It was thus considered that … , … . (Result)
- The panel of … lines nevertheless represents a … set of … , with … from Africa (… , … , … ; apart from … that was originally supposedly African but was identical to … here), 7 from South East Asia (… , … , … , … , … , … , and … that are almost identical clones from the same isolate), 2 from Papua New Guinea (… and … with apparently shared clonal history in culture), one isolate from South America (… ), one from Central America (… ), and one (… ) which was cloned from isolate … derived from a case of airport malaria in The Netherlands presumed to be acquired from the bite of an infected African mosquito. (Context)
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