Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.

中文翻译：

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使用 PSI 扩展 FASTA 格式扩展 Comet 以进行全局氨基酸变体和翻译后修饰分析。

通过串联质谱序列数据库搜索进行蛋白质鉴定是许多蛋白质组学实验室的标准做法。用作序列数据库搜索工具输入的序列数据库表示的事实标准是 FASTA 格式。人类蛋白质组组织的蛋白质组标准倡议开发了 FASTA 格式的扩展，称为蛋白质组标准倡议扩展 FASTA 格式或 PSI 扩展 FASTA 格式 (PEFF)，其中结构注释等附加信息编码在蛋白质描述行中。Comet 已扩展为自动分析 PEFF 数据库中编码的翻译后修饰和氨基酸取代。介绍了 Comet 的 PEFF 实现以及根据 neXtProt PEFF 数据库搜索 HEK293 数据集的示例分析结果。