P-mod: An algorithm and software to map modifications to peptide sequences using tandem MS data
P-mod: An algorithm and software to map modifications to peptide sequences using tandem MS data
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DOI：
10.1021/pr0498234
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发表时间：
2005-03-01
影响因子：
4.4
通讯作者：
Liebler, DC
中科院分区：
文献类型：
--
作者：
Hansen, BT;Davey, SW;Liebler, DC
蛋白质组学中最具挑战性的问题之一是发现蛋白质的非预期修饰。虽然广泛使用的算法（例如Sequest和Mascot）能够在质量和氨基酸特异性已知时对修饰进行映射，但无法使用这些工具识别意外的修饰。我们已经开发了一种称为P-Mod的算法和软件，该算法和软件能够发现和序列映射已知在分析中表示或通过Sequest识别的靶蛋白的修饰。P-Mod将MS/MS光谱与搜索列表中的肽序列进行匹配。对于修饰肽的光谱，P-Mod计算搜索肽序列和MS/MS前体之间的质量差，并将质量偏移定位到肽中的序列位置。由于修饰被检测为质量偏移，因此P-Mod不需要用户猜测修饰的质量或序列位置。P-Mod使用极值统计将p值估计分配给序列到频谱匹配。对报告的p值进行缩放以说明比较的数量，使得错误率不会随着并入潜在肽修饰而产生的扩展搜索列表而增加。来自多个LC-MS/MS分析和多个样品的P-Mod搜索的组合揭示了先前未报道的BSA修饰，包括蛋白质的位置579处的新的脱羧甲基化或D -> G取代。P-Mod可以在鉴定外源性和内源性来源的蛋白质修饰中发挥独特的作用，并且可以用于鉴定修饰的蛋白质形式作为毒性和疾病过程的生物标志物。
The discovery of unanticipated protein modifications is one of the most challenging problems in proteomics. Whereas widely used algorithms such as Sequest and Mascot enable mapping of modifications when the mass and amino acid specificity are known, unexpected modifications cannot be identified with these tools. We have developed an algorithm and software called P-Mod, which enables discovery and sequence mapping of modifications to target proteins known to be represented in the analysis or identified by Sequest. P-Mod matches MS/MS spectra to peptide sequences in a search list. For spectra of modified peptides, P-Mod calculates mass differences between search peptide sequences and MS/MS precursors and localizes the mass shift to a sequence position in the peptide. Because modifications are detected as mass shifts, P-Mod does not require the user to guess at masses or sequence locations of modifications. P-Mod uses extreme value statistics to assign p value estimates to sequence-to-spectrum matches. The reported p values are scaled to account for the number of comparisons, so that error rates do not increase with the expanded search lists that result from incorporating potential peptide modifications. Combination of P-Mod searches from multiple LC-MS/MS analyses and multiple samples revealed previously unreported BSA modifications, including a novel decarboxymethylation or D -> G substitution at position 579 of the protein. P-Mod can serve a unique role in the identification of protein modifications both from exogenous and endogenous sources and may be useful for identifying modified protein forms as biomarkers for toxicity and disease processes.