Evaluation of the Synthetic Product

In 1987, an article appeared in the International Journal of Peptide and Protein Research commemorating the 25th anniversary of the development of solid phase peptide synthesis (Barany et al., 1987). While that article dealt with many aspects of peptide synthesis, one statement in particular stands out as exemplifying the rationale for this chapter. It states: “No synthetic endeavor can be considered complete until the product has been adequately purified and subjected to a battery of analytical tests to verify its structure.” The characterization or evaluation of a synthetic peptide is the one step in its production and experimental utilization that will validate the experimental data obtained. Unfortunately, it is also the one step that many investigators all too often give too little attention. If the synthetic product, upon which the theory and performance of the experimental investigation is based, is not the intended product, the conclusions will be incorrect. Without proper characterization, the investigator will either have to be lucky, or be wrong. Worse yet, he or she will not know which is the case. Although today the synthesis of a given peptide is often considered routine, the product should never be taken for granted. Peptide synthesis chemistry, although quite sophisticated, is complex and subject to a variety of problems. These problems, which can manifest themselves as unwanted side reactions and decreased reaction efficiency, are subject to a variety of factors such as reagent quality, incompatible chemistries, instrument malfunctions, sequence specific effects, and operator error. Although every effort is made to eliminate their causes and to plan for potential problems in the design and synthesis steps, it is not always successful and the eventual outcome of a synthesis is not always predictable. One must never assume that the final product is the expected one until that has been proven to be the case. To do otherwise may seriously jeopardize the outcome of the research. Used and performed properly, the evaluation stage is where the fruits of the synthesis are scrutinized and the decision is made to use the peptide as intended, submit it to further purification, or resynthesize it and possibly change elements of the design or synthesis protocols.