Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines.

中文翻译：

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数据库搜索引擎的剖析与发展-基于质谱的蛋白质组学工作流的核心组成部分

序列数据库搜索引擎是生物信息学算法，可使用参考蛋白质序列数据库从串联质谱图中识别肽段。经过二十年的发展，特别是在质谱技术的发展推动下，已经为科学家提供了30多个已发布的搜索引擎，每个搜索引擎都有其自己的属性。在这篇综述中，我们介绍了不同实现背后的共同范例，以及它对现代质谱数据集的局限性。我们还将详细介绍搜索引擎如何尝试减轻这些限制，并概述可供研究人员使用的不同软件框架。最后，我们着重介绍了用于鉴定蛋白质组质谱数据集的替代方法，以替代或补充序列数据库搜索引擎。