Have you ever looked at the Materials and Methods section of a research paper to try and find details of a protocol you want to implement in the lab? Have you come across short paragraphs that concisely summarize a method but leave out critical details? Have you found yourself asking questions like:
- How long did they spin those samples for?
- Did they store the overnight suspension in a fridge or freezer?
- Exactly which ultra high metal affinity column did they purchase?
If you answered yes to any of these, don’t be alarmed – you are not alone.
The art of writing a precise yet detailed and contextualized, relatable and reproducible protocol has far too often been confined to a lab notebook that will never again be seen by anybody other than the lab notebook owner and a handful of their colleagues.
This article will share some pointers that provide a framework for writing an easily reproducible protocol.
Structure as a whole
It is important to think of a protocol (may it be wet or dry lab-based, biology or chemistry-focused, simple or advanced) as a brief, modular and self-contained scientific publication. To this end, several factors can be considered when preparing a draft.
Putting the methodology in context
You never know who will refer to your protocol in the future. It may be a new graduate student joining the lab you’re preparing to leave or a new postdoc joining several years later when you’re a busy and established PI thousands of miles away possibly researching something entirely different. Alternatively, it may be a researcher you have never met who is working on a different species but looking for a protocol they can adapt for their needs. Whoever it may be, they will likely benefit from reading a three- to four-sentence abstract at the onset that briefly explains the system you worked on, describes any major obstacles or challenges you faced, and highlights the applicability of your workflow.
Materials and tools that were used in the protocol
Lets face it: two different batches of agarose or of magnesium sulfate may not be the same. Commonly used biochemical reagents could vary in terms of purity, yield, pH, hydration state, grade, and possibly additional biochemical or biophysical features. For many researchers this may not matter; yet for others it may be a deal breaker in terms of implementing your protocol into their workflow.
Similarly, when you mention “centrifuge,” this may not indicate how fast it can spin or how cold it can keep your samples. When a researcher finds out half way through an experiment that the process they set up based on your protocol cannot be completed because a simple detail was missing, the outcome is frustrating for everyone concerned.
This can lead to a poor reflection of your protocol, wasted resources in the lab, and time and effort that could have been better utilized. Share as many details as you can, such as catalog numbers and manufacturer details.
A chronology of steps
Bullet points are easy to follow and help others track a particular workflow. Always think about exactly what you did when you were using your protocol in the lab, and that the person using your protocol may be a novice experimenter.
Think about the quantities you used, sample replication, storage conditions, spinning and mixing, and details on how to operate various instruments and equipment. Listing all steps in a chronological and modular fashion can be a very effective interface for researchers that are trying to implement your protocol within their own laboratory workflows.
Notes, recipes, tips, and tricks
I would recommend wrapping up your protocol draft with a brief section that highlights details you might take for granted. Sometimes it is the little things that make an experiment work, flicking a tube gently versus vortexing it, spraying water on a leaf surface before infiltrating it with a syringe, or using PBS and tweezers to remove glue from a piece of sliced gel.
These are exactly the types of simple tricks or “secret sauce” that can save researchers weeks and potentially months of time and effort in the successful implementation of a protocol.
A well-curated database of protocols can serve as the backbone of a high performing research laboratory. There are a growing number of resources such as Bio-protocol and Protocols.io that allow you to share your protocols effectively with the research community and build your own portfolio of research methodologies.
Resources such as these as well as other established protocol journals and organizations such as JOVE, Science Exchange, COS, and GBSI are filling an important niche to ensure that the scientific community maintains its core mission of delivering reproducible results.