Background: The identification of non-specifically cleaved peptides in proteomics and peptidomics poses a significant computational challenge. Current strategies for the identification of such peptides are typically time-consuming and hinder routine data analysis.

Objective: We aimed to design an algorithm that would improve the speed of semi- and nonspecific enzyme searches and could be applied to existing search programs.

Methods: We developed a novel search algorithm that leverages fragment-ion redundancy to simultaneously search multiple non-specifically cleaved peptides at once. Briefly, a theoretical peptide tandem mass spectrum is generated using only the fragment-ion series from a single terminus. This spectrum serves as a proxy for several shorter theoretical peptides sharing the same terminus. After database searching, amino acids are removed from the opposing terminus until the observed and theoretical precursor masses match within a given mass tolerance.

Results: The algorithm was implemented in the search program MetaMorpheus and found to perform an order of magnitude faster than the traditional MetaMorpheus search and produce superior results.

Conclusion: We report a speedy non-specific enzyme search algorithm that is open-source and enables search programs to utilize fragment-ion redundancy to achieve a notable increase in search speed.

背景：蛋白质组学和肽组学中非特异性切割肽的鉴定是一项重大的计算挑战。目前用于识别此类肽的策略通常非常耗时并且阻碍了常规数据分析。

目的：我们旨在设计一种算法，可以提高半特异性和非特异性酶搜索的速度，并可以应用于现有的搜索程序。

方法：我们开发了一种新的搜索算法，该算法利用片段离子冗余同时搜索多个非特异性切割的肽。简而言之，仅使用来自单个末端的片段离子系列生成理论肽串联质谱。该光谱可作为几个较短的理论肽共享相同末端的代理。数据库搜索后，从相反的末端去除氨基酸，直到观察到的和理论的前体质量在给定的质量公差内匹配。

结果：该算法在搜索程序 MetaMorpheus 中实施，发现其执行速度比传统的 MetaMorpheus 搜索快一个数量级，并产生出色的结果。

结论：我们报告了一种快速的非特异性酶搜索算法，它是开源的，使搜索程序能够利用碎片离子冗余来显着提高搜索速度。