Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Hong Kong, PR China.
Proteomics. 2011 Dec;11(24):4702-11. doi: 10.1002/pmic.201100316. Epub 2011 Nov 23.
Spectral library searching is a promising alternative to sequence database searching in peptide identification from MS/MS spectra. The key advantage of spectral library searching is the utilization of more spectral features to improve score discrimination between good and bad matches, and hence sensitivity. However, the coverage of reference spectral library is limited by current experimental and computational methods. We developed a computational approach to expand the coverage of spectral libraries with semi-empirical spectra predicted from perturbing known spectra of similar sequences, such as those with single amino acid substitutions. We hypothesized that the peptide of similar sequences should produce similar fragmentation patterns, at least in most cases. Our results confirm our hypothesis and specify when this approach can be applied. In actual spectral searching of real data sets, the sensitivity advantage of spectral library searching over sequence database searching can be mostly retained even when all real spectra are replaced by semi-empirical ones. We demonstrated the applicability of this approach by detecting several known non-synonymous single-nucleotide polymorphisms in three large human data sets by spectral searching.
谱库检索是一种很有前途的方法，可以替代序列数据库检索，用于从 MS/MS 谱中鉴定肽。谱库检索的主要优势在于利用更多的谱特征来提高良好匹配与不良匹配之间的得分区分度，从而提高灵敏度。然而，参考谱库的覆盖范围受到当前实验和计算方法的限制。我们开发了一种计算方法，通过从类似序列的已知谱中扰动来扩展谱库的覆盖范围，例如具有单个氨基酸取代的谱。我们假设类似序列的肽应该产生类似的片段模式，至少在大多数情况下是这样。我们的结果证实了我们的假设，并确定了何时可以应用这种方法。在实际的真实数据集的谱搜索中，即使所有的真实谱都被半经验谱所取代，谱库搜索的灵敏度优势仍能在很大程度上保留。我们通过在三个大型人类数据集的谱搜索中检测到几个已知的非同义单核苷酸多态性，证明了这种方法的适用性。
