Nuts and bolts (a short guide to writing Materials & Methods sections)

Lab Bench_ArtandScience2020.jpg
“Lab bench” by Dorotea Fracchiolla

Clear Materials and Methods sections are essential for other scientists to reproduce your work. Here’s a short guide on how to write them.

We already have a “How to…” posting on writing complete project reports/papers, but today we’re going to zero in on one section in particular: the Materials and Methods. There are some minor variations depending on whether you’re writing a thesis or a research paper (we’ll deal with them later on), but the general approach is the same for both.

In essence, the purpose of the Materials & Methods is to enable someone reading it to exactly repeat what you’ve done (and hopefully get the same results). If you’re ever in doubt after finishing this section, ask yourself, or ask a colleague, if it would be possible to recapitulate your work based only on the information you’re providing. If that’s not the case, then you need to make some edits.

Stylistically, there’s probably more variation in Materials & Methods sections than in the other elements of a research paper or project report, and the ultimate purpose is pragmatic – as long as you’ve been clear on what you’ve done, you’re ok. Think of this guide then not as a rigid prescription, but more as a pointer if you’re having trouble getting started or if you are unhappy with what you’ve produced so far.

One of the few hard rules with Materials & Methods is that, like the Results section, it is always written in the past tense. Unlike the Results, it should also always be in the passive voice (“the fractions were separated…” instead of “we separated the fractions…”).

A simple formula for a methods paragraph is as follows:
The [material] was/were [treated] by/with/using [process/buffer/reagent/chemical] (condition, time, temperature).

For example:
The liposomes were pelleted by centrifugation (10,000 xg, 10 min, 4°C).
The lysates were separated using SDS-PAGE (200V, 60 min, RT).
The Golgi was detected using anti-GRASP antibodies (60 min, RT)
The ORF was amplified by PCR.
The cells were fixed using ice-cold methanol (30 min, -20°C)

For subsequent steps, the same formula can be repeated, with the addition of linking words/phrases:
Next, the [material] was [treated]…
The [material] was then [treated]…
The [material] was then resuspended in [solution], and [treated]…

One advantage of this formula is that it allows different verbs to be used for the same technical process. This is useful because the same process can often be used for achieving different results. Consider centrifugation:
The cells were harvested by centrifugation
The liposomes were pelleted by centrifugation
The solution was clarified by centrifugation
The fractions were separated by centrifugation

“To centrifuge” is actually a recognised verb, but note how much more informative the use of the verb+centrifugation formula is. It immediately focuses the reader’s attention on whether it’s the pellet, the supernatant, or both that’s most relevant at that time, and it tells the reader why you carried out the process.

“To electrophorese” is another recognised verb which should probably be avoided.
The PCR products were visualised using agarose gel electrophoresis
The DNA fragments were separated using agarose gel electrophoresis
The capping assays were analysed using polyacrylamide gel electrophoresis

Some handy verbs for treatments are:
aliquoted, amplified, analysed, blocked, bound, captured, checked, clarified, confirmed, denatured, detected, dialysed, fixed, harvested, incubated, labelled, mixed, mounted, pelleted, permeabilised, precipitated, quantified, released, resuspended, rinsed, separated, transformed, transferred, validated, visualised, washed.

Be careful to avoid lab slang: “to run on a gel” and “to PCR something” are commonly heard, but should never be in a methods section. And never, ever say “the DNA was transformed into bacteria” – this is not only slang, it’s also inaccurate and biologically impossible. Instead:
The DNA was used to transform bacteria.
The DNA was amplified by PCR.
The DNA was visualised using agarose gel electrophoresis.

If you’re short on space it is acceptable to cite a previous publication instead.
The [procedure] was carried out as previously described (Author1 et al., [year]).

If you are forced to use this shortcut however, never just leave it at that. Always follow it with, “In brief, this involved…” and then provide as long a summary of the method as space will allow, omitting things like time/temperature/conditions and so on. Otherwise a reader has to go and look up another paper just to get an idea of what you’ve done, and that’s not helpful – especially if it relates to important data.

Don’t forget to provide correct units and concentrations. Always provide x g and not rpm for centrifugation steps. Always provide the conjugate acid/base for pH buffers (Tris-HCl pH 6.8 not Tris pH 6.8).

For all methods, don’t forget to include details on how many technical replicates, biological replicates, and independent experiments were done (if you’re unclear on the difference between these terms, check out our short guide on that topic).

There is always a degree of overlap between Materials & Methods sections and figure legends. Figure legends can be used to provide specifics and the Materials & Methods a more general outline if the same general method is used in a number of variations in a single study. Alternatively, the figure legends can provide an overview of the method (similar to the “In brief…” point above) while the Materials and Methods provides the hard details on concentrations, washes, and so on.

Generally speaking, it is not necessary to cite a supplier if a reagent or equipment is pretty standard (centrifuges, electrophoresis rigs, standard chemicals), but the supplier should always be listed if the product is specialised (e.g. an ultra-pure variety of a chemical ) or if there’s sufficient variation between competing products to make listing it relevant (antibodies, chromatography columns, and so on).

One of the biggest factors influencing the length and content of a Materials & Methods section is whether you’re writing a thesis or a research paper.

If you’re writing a thesis, it’s simple: you include EVERYTHING. Every single technique and assay and approach you tried, even if it was used very rarely. This is because a large part of your training is spent acquiring practical skills, and your Materials and Methods section is therefore both a means of advertising what techniques you have first-hand experience of, and documenting what you did.

In research papers, there is always a bit of a trade-off depending on whether the intended reader is a specialist or a generalist – making something intelligible to literally everybody would mean writing a textbook, but omitting too much looks slapdash and complacent. Judging the right level of detail and inclusion comes with practice.

As with any science writing, you should always be asking yourself if there’s a way that you can be more precise. Philosophically speaking, it’s probably (almost) impossible to write a sentence that’s totally unambiguous, but you can try your hardest to be close to that. Have fun trying, and good luck!

Disclaimer: As always, we’re primarily drawing on biomedical research here as this is TIR’s main area of expertise, but hopefully a lot of these recommendations are applicable more generally.

Artwork: this week’s artwork is from first-time TIR contributor Dorotea Fracchiolla. Doro writes, “I’m a molecular biologist with a passion for art. I actually can’t tell what came first but since my illustrations date back to childhood I´d say I was first an artist, and then I became a scientist. I recently created Art&Science, my personal art space where by learning recent advances in science I can feed my curiosity, express my creativity, and spice it up with a personal view of the world at a molecular level. During my carrier as a scientist, I always tried to translate ideas into drawings, as for me this is the best way to define things: making them visible! It helps me finding out what’s the missing piece. I´d love to help other scientists to do so and that’s what Art&Science is here for!”

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