This is part of a tutorial series I’m writing for my students on scientific manuscript preparation. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.
This section should include information on every experimental procedure used in the work. You don’t have to include experimental details of everything that was in your lab notebook or all of the optimization work you did for the project. Yeah, readers don’t care about the two-years’ worth of failed protein purification methods in your notebook. You will only include the short paragraph of what did finally work. Refer to your figures. Whatever experiments yielded data that is ultimately found in your figures should have details in your Materials and Methods section. If certain reagents were critical to completion of the experiments, then include your sources for them (commercial or donations from other labs). The Materials and Methods section is written in the past tense without the use of personal pronouns. It may seem awkward to get into this point of view, but there is an omniscient perspective from which your methods can be written. I’m not sure where this convention originated, but remove yourself from the experiment and it seems more legitimate.
Subdivide this section into useful parts. This kind of organization also helps the reader pinpoint details for replication or evaluation of experiments. Often readers will be looking at your work to perform similar experiments or repeat your work.
It’s not exactly a protocol, but it should be complete. You don’t have to tell your readers every step of a protocol, but it should be complete enough for someone else with comparable training to replicate. The literature varies widely in the usefulness and clarity of methods descriptions. For more complex procedures, authors are often contacted directly for lab protocols or additional information not included in the materials and methods section. As methods have become more complex, fewer details are included. This is especially true of molecular biology work. Typically primer sequences are given and specific vectors are mentioned, but it can be especially irksome to figure out others’ cloning construction strategies. Usually, though, this information can be obtained directly from the authors. In general, I would err on the side of completeness (vs. concise) because this makes it easier for your experimental strategies to be evaluated and replicated. This strategy can run afoul of the journal’s character limits, but in this age of online publication, supplemental information is allowed. You can write a ‘Supplemental Methods’ section which will be available online only and can be as long as you’d like.
Referencing previous literature is a convenient way of being concise. It is acceptable to say something like, “This experiment was performed as in Reference (1).” However, if you go this route, make sure that the reference you are citing in this case does have the necessary information on experimental details. The scientific literature is infamous for pulling this trick only to reference yet another paper that says “This experiment was performed as in Reference (2).” You may have to follow this rabbit hole back a couple of decades before you find any real useful information on performing the experiment. (This is a personal pet peeve of mine that just makes me feel stabby when I encounter this nonsense.) So save your readers some trouble and either include the necessary info or cite a direct source. For many labs, there are standard references and descriptions for routinely used methods that appear in almost all of the manuscripts. It’s fine to revert back to previously published articles to see how things were worded and what references were cited, but it’s always a good idea to verify these references yourself. Otherwise, a mis-referenced citation will be propagated many times over. (This is also a good practice for any citation anywhere in a manuscript- to make sure the reference is really saying what you think it does.)
Offer your pro-tips for methods-writing in the comments section below.