用以确定抗原表位的最短长度，通过系统性地截取两侧末端氨基酸获得。一般与丙氨酸筛查肽库结合使用，在使用丙氨酸确定表位关键残基后，截头肽库用来进一步确定最短表位序列及其作用。
在许多案例中，截头肽库用于可鉴定筛选增强蛋白水解作用的多肽。它可以作为研究多肽药物代谢降解程度的工具。
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