蛋白胺基酸是指在蛋白质内可找到且编码在标准遗传密码中的二十种胺基酸。

非蛋白胺基酸则是指在蛋白质内找不到（如carnitine、GABA和L-DOPA），或没有被标准遗传密码编码（如羟脯胺酸和硒甲硫氨酸）的其他胺基酸。后者通常源自于蛋白质的转译后修饰作用。

某些非蛋白胺基酸（如鸟氨酸和en:homoserine）对于生物缺少将其组进蛋白质内的功能有着很清楚的根本因素；如前面所举的两个胺基酸就会cyclize against the peptide backbone and fragment the protein with relatively short half-lives.

Proteinogenic amino acids are amino acids that are precursors to proteins, and are incorporated into proteins during translation. Throughout known life, there are 23 proteinogenic amino acids, 20 in the standard genetic code and an additional 3 that can be incorporated by special translation mechanisms. Both eukaryotes and prokaryotes can incorporate selenocysteine into their proteins via a nucleotide sequence known as a SECIS element, which directs the cell to translate a nearby UGA codon as selenocysteine (UGA is normally a stop codon). In some methanogenic prokaryotes, the UAG codon (normally a stop codon) can also be translated to pyrrolysine. In bacteria, the AUG initiation codon is translated to N-formylmethionine when it is actually used to initiate translation and translated normally (to methionine) at other times. In eukaryotes, there are only 21 proteinogenic amino acids, the 20 of the standard genetic code, plus selenocysteine. Humans can synthesize 12 of these from each other or from other molecules of intermediary metabolism. The other nine must be consumed (usually as their protein derivatives), and so they are called essential amino acids. The essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (i.e. H I L K M F T W V).