Abstract The application of database search algorithms with very wide precursor mass tolerances for the “Open Search” paradigm has brought new efforts at post-translational modification discovery in shotgun proteomes. This approach has motivated the acceleration of database search tools by incorporating fragment indexing features. In this report, we compare open searches and sequence tag searches of high-resolution tandem mass spectra to seek a common “palette” of modifications when analyzing multiple formalin-fixed, paraffin-embedded (FFPE) tissues from Thermo Q-Exactive and SCIEX TripleTOF instruments. While open search in MSFragger produced some gains in identified spectra, careful FDR control limited the best result to 24% more spectra than narrow search (worst result: a loss of 9%). Open pFind produced high apparent sensitivity for PSMs, but entrapment sequences hinted that the actual error rate may be higher than reported by the software. Combining sequence tagging, open search, and chemical knowledge, we converged on this set of PTMs for our four FFPE sets: mono- and di-methylation (nTerm and Lys), single and double oxidation (Met and Pro), and variable carbamidomethylation (nTerm and Cys).

中文翻译：

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公开搜索揭示了福尔马林固定、石蜡包埋的热 HCD 和 SCIEX TripleTOF 霰弹枪蛋白质组中的修饰模式

摘要 具有非常宽前体质量容差的数据库搜索算法在“开放搜索”范式中的应用为鸟枪蛋白质组中的翻译后修饰发现带来了新的努力。这种方法通过结合片段索引功能促进了数据库搜索工具的加速。在本报告中，我们比较了高分辨率串联质谱的开放搜索和序列标签搜索，以在分析来自 Thermo Q-Exactive 和 SCIEX TripleTOF 的多个福尔马林固定、石蜡包埋 (FFPE) 组织时寻找常见的修饰“调色板”仪器。虽然 MSFragger 中的开放搜索在已识别的光谱中产生了一些收益，但仔细的 FDR 控制将最佳结果限制在比窄搜索多 24% 的光谱（最坏结果：损失 9%）。Open pFind 对 PSM 产生了很高的表观灵敏度，但诱捕序列暗示实际错误率可能高于软件报告的错误率。结合序列标记、开放搜索和化学知识，我们为我们的四个 FFPE 集聚合了这组 PTM：单和二甲基化（nTerm 和 Lys）、单和双氧化（Met 和 Pro）以及可变氨基甲酰甲基化（ nTerm 和 Cys）。