Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.
Proteomics. 2019 Sep;19(17):e1800444. doi: 10.1002/pmic.201800444. Epub 2019 Aug 8.
High-resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, MS2-Deisotoper, a tool for use prior to database search, is used to identify monoisotopic peaks in centroided MS/MS spectra. MS2-Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimization, it is shown that MS2-Deisotoper can improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It is effective with SILAC and non-SILAC MS/MS data. The identification of unique peptide sequences is also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results shows that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs, and leads to greater protein sequence coverage. At a peptide level, it is found that the efficacy of deisotoping is affected by peptide mass and charge. MS2-Deisotoper can be used via a user interface or as a command-line tool.
高分辨率 MS/MS 谱图的肽段可以去同位素峰，以鉴定肽片段的单一同位素质量。使用这种质量应该可以提高蛋白质鉴定率。然而，去同位素峰处理并非普遍使用，其好处也尚未得到充分探索。这里，我们使用了 MS2-Deisotoper 这个在数据库搜索之前使用的工具，以鉴定质心 MS/MS 谱图中的单一同位素峰。MS2-Deisotoper 的工作原理是比较每个肽段峰的质量和相对强度与其他质量较大的峰，同时应用一组关于质量和强度差异的规则。经过全面的参数优化，结果表明 MS2-Deisotoper 可以将鉴定的肽谱匹配 (PSMs) 数量提高多达 8.2%，蛋白质数量提高多达 2.8%。它对 SILAC 和非 SILAC MS/MS 数据都有效。独特肽序列的鉴定也得到了改善，人类蛋白异构体的数量增加了 3.7%。对结果的详细调查表明，去同位素峰处理可以提高 Mascot 离子得分，改善 PSMs 的 FDR 估计，并提高蛋白质序列的覆盖率。在肽水平上，发现去同位素峰处理的效果受肽质量和电荷的影响。MS2-Deisotoper 可以通过用户界面或命令行工具使用。
