Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer
Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer
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LTQ Orbitrap Velos 质谱仪上胰蛋白酶肽的 HCD 碎片模式的统计表征。
DOI：
10.1016/j.jprot.2014.06.012
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发表时间：
2014-09-23
影响因子：
3.3
通讯作者：
Sun, Wei
中科院分区：
文献类型：
--
作者：
Shao, Chen;Zhang, Yang;Sun, Wei
高能碰撞解离(HCD)是Orbitrap质谱仪中广泛使用的一种高效的多肽裂解方法。更好地理解HCD碎片模式将有助于蛋白质组数据分析算法的发展。在这项研究中，在LTQ Orbitrap Velos质谱仪上统计地描述了HCD模式下B和Y离子的碎裂模式和残基特定的切割效应。我们比较了在轨道捕获装置中收集的相同双电荷和三电荷胰蛋白酶多肽的HCD和CID光谱。我们的分析结果揭示了HCD光谱的新的统计特征。Y离子的强度分别在双电荷肽和三电荷肽的HCD谱的60-70%和40-50%相对质量区段达到最大。与CID模式相比，HCD模式更倾向于产生电荷更低的Y离子。在HCD谱中，5种碎片离子以单电荷碎片离子为主，强度最高。B离子的疏水残基是两种模式切割选择性的主要差异，而y离子的疏水残基表现出相似的切割偏好。这些结果将有助于数据库搜索引擎的开发和针对靶向蛋白质组分析的适当过渡的设计。生物学意义Orbitrap MS正在成为蛋白质组分析的流行工具，而HCD模式以其高分辨率和高灵敏度正成为主要的分析模式。本研究通过与LTQ Velos Orbitrap上的CID模式进行比较，表征了HCD谱的特征。首次系统地比较了HCD和CID两种模式下B和Y离子的带电状态、离子频率和强度以及解离选择性。这些结果将有助于开发数据库搜索引擎，并为未来的目标蛋白质组分析设计适当的过渡。(C)2014爱思唯尔B.V.保留所有权利。
High-energy collisional dissociation (HCD) is an efficient peptide fragmentation method that is widely used in Orbitrap mass spectrometers. A greater understanding of HCD fragmentation patterns would benefit the development of proteomic data analysis algorithms. In this study, b and y ion fragmentation patterns and residue-specific cleavage effects in HCD mode were statistically characterized on a LTQ Orbitrap Velos mass spectrometer. We compared HCD and CID spectra collected in an Orbitrap for the same doubly and triply charged tryptic peptides. Our analytical results revealed novel statistical features of HCD spectra. The intensity of y ions reached a maximum in the 60-70% and 40-50% relative mass bins of HCD spectra from doubly and triply charged peptides, respectively. The HCD mode showed a slight preference for generating y ions with lower charges than did CID mode. Singly charged fragment ions dominated the five fragment ions with the highest intensity in HCD spectra. Hydrophobic residues for b ions were the primary differences in cleavage selectivity between the two modes, while residues for y ions showed a similar cleavage preference. These results will assist with the development of database search engines and the design of proper transitions for targeted proteomic analysis.Biological significanceOrbitrap mass spectrometry is becoming the popular instrument for proteomic analysis, and HCD mode is becoming the main analysis mode for its high resolution and high sensitivity. This study characterizes the features of HCD spectrum by comparing with CID mode on LTQ Velos Orbitrap. The patterns of b and y ions in HCD and CID modes were systematically compared for the first time, including the charge state, ion frequency and intensity and cleavage selectivity. These results will help develop database search engines and design proper transitions for targeted proteomic analysis in the future. (C) 2014 Elsevier B.V. All rights reserved.