A control experiment is one that is treated in the same way as an actual experiment, but is not exposed to the experimental agent. There are two types of controls for experiments, positive and negative controls. A positive control experiment is one that uses an agent known to produce a quantifiable and well understood effect on the system. In contrast, a negative control experiment is one that uses the same procedures as the actual experiment, but has no extra treatment or uses an agent that is expected to be inactive.
In peptide experiments, negative controls are frequently used to demonstrate that a specific sequence of a peptide, rather than its amino acid composition is critical for activity. Scrambled, or shuffled, or randomly rearranged sequences are widely used in place of the active agent while other properties such as molecular weight or peptide chain length are kept are the same. So long as the control experiment is treated virtually identically to the actual experiment, the comparison increases confidence that any difference in outcome is caused by the presence of the specific peptide sequence and is not an artifact.