蛋白质组学
计算生物学
计算机科学
翻译后修饰
碎片(计算)
数据库搜索引擎
鸟枪蛋白质组学
质谱法
蛋白质基因组学
半胱氨酸
化学
肽
生物化学
生物
搜索引擎
基因组学
色谱法
基因组
情报检索
基因
酶
操作系统
作者
Daniel Geiszler,Daniel A. Polasky,Fengchao Yu,Alexey I. Nesvizhskii
标识
DOI:10.1038/s41467-023-39828-0
摘要
Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge in methods to detect them in recent years. However, post-translational modifications can introduce complexity into proteomics searches by fragmenting in unexpected ways, ultimately hindering the detection of modified peptides. To address these deficiencies, we present a fully automated method to find diagnostic spectral features for any modification. The features can be incorporated into proteomics search engines to improve modified peptide recovery and localization. We show the utility of this approach by interrogating fragmentation patterns for a cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, and ADP-ribosylated peptides. We also analyze the interactions between a diagnostic ion's intensity and its statistical properties. This method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
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