In the natural sciences, the terms protocol and method (as distinct from scientific method) are often used interchangeably. Both are documents that detail how to do the work required to obtain meaningful scientific results. This work might be an analytical technique, the synthesis of a chemical compound or the set up of equipment. The term natural science as the way in which different fields of study are defined is determined as much by historical convention as by the present day meaning of the words. ... This article or section does not cite its references or sources. ... Scientific method is a body of techniques for investigating phenomena and acquiring new knowledge, as well as for correcting and integrating previous knowledge. ...

The defining feature of a protocol, however, is that the procedure is formatted as a series of numbered steps similar to that seen in recipe books - the materials (reagents and equipment) are listed separately.

Structurally, it has much in common with a standard operating procedure (SOP), though its purpose / role in the scientific process is different. Both should give guidelines regarding, for example, the number of replicates required to get statistically meaningful results or the appropriate negative and positive controls. Protocols can highlight steps that are optional or that should be optimized in the experimenters’ laboratories, as well as giving advice on how to adapt the procedure if the purpose of the experiment changes. An SOP, however, is a highly optimized protocol standardized in the laboratory in which it is performed, that has been designed to be followed exactly in order to conform with industry standards or regulations. Standard Operating Procedure(s) or SOPs (pronounced letter by letter, ie ESS OH PEE(s) ) is a military term used to describe a procedure or set of procedures to perform a given operation or evolutions or in reaction to a given event. ...

There are many scientific journals that publish methods and protocols. There are also open-access sites where researchers can download their protocols and many research groups publish their protocols on their websites. Examples of these are listed below:

Open-access sites

• SyntheticPages
• TAIR Protocol Search (is part of the The Arabidopsis Information Resource site)
• Nature Protocols also has section called Protocols Network where researchers are invited to upload their protocols. These protocols are freely available.

Scientific Journals

• CSH Protocols
• Nature Protocols
• Nature Methods
• Current Protocols
• Methods
• Analytical Chemistry
• Analytical biochemistry
• Organic synthesis