pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
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pNovo：使用 HCD 光谱进行从头肽测序和鉴定
DOI：
10.1021/pr100182k
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发表时间：
2010-05-01
影响因子：
4.4
通讯作者：
Dong, Meng-Qiu
中科院分区：
文献类型：
--
作者：
Chi, Hao;Sun, Rui-Xiang;Dong, Meng-Qiu
在过去的十年中，由于更好的仪器和计算算法，从头肽测序有了显着的改进。然而，从头测序只能正确解释近似30%的碰撞诱导解离（CID）产生的高质量和中等质量光谱，这比数据库搜索要少得多。这主要是由于CID谱中不同离子系列的不完全碎裂和重叠造成的。在这项研究中，我们表明，高能碰撞解离（HCD）是很大的帮助，从头测序，因为它产生高质量的准确度串联质谱（MS/MS）光谱，而没有低质量截止与CID在离子阱仪器。此外，HCD谱中丰富的内离子和亚铵离子有助于区分相似的肽序列。利用这些特点，我们开发了一种称为pNovo的算法，用于从HCD光谱中对肽进行有效的从头测序。pNovo对通过数据库检索鉴定的80%或更多的HCD光谱进行了正确鉴定。通过pNovo测序的正确全长肽的数量与通过数据库检索获得的数量相当。从头测序的一个明显优势是脱酰胺肽和具有氨基酸突变的肽可以有效地鉴定，而无需额外的计算成本。总之，HCD特征的实现使pNovo成为从HCD谱进行从头肽测序的优秀工具。
De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de novo sequencing can correctly interpret only similar to 30% of high- and medium-quality spectra generated by collision-induced dissociation (CID), which is much less than database search. This is mainly due to incomplete fragmentation and overlap of different ion series in CID spectra. In this study, we show that higher-energy collisional dissociation (HCD) is of great help to de novo sequencing because it produces high mass accuracy tandem mass spectrometry (MS/MS) spectra without the low-mass cutoff associated with CID in ion trap instruments. Besides, abundant internal and immonium ions in the HCD spectra can help differentiate similar peptide sequences. Taking advantage of these characteristics, we developed an algorithm called pNovo for efficient de novo sequencing of peptides from HCD spectra. pNovo gave correct identifications to 80% or more of the HCD spectra identified by database search. The number of correct full-length peptides sequenced by pNovo is comparable with that obtained by database search. A distinct advantage of de novo sequencing is that deamidated peptides and peptides with amino acid mutations can be identified efficiently without extra cost in computation. In summary, implementation of the HCD characteristics makes pNovo an excellent tool for de novo peptide sequencing from HCD spectra.