Influence of basic residue content on fragment ion peak intensities in low-energy - collision-induced dissociation spectra of peptides
Influence of basic residue content on fragment ion peak intensities in low-energy - collision-induced dissociation spectra of peptides
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DOI：
10.1021/ac0351163
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发表时间：
2004-03-01
影响因子：
7.4
通讯作者：
Yates, JR
中科院分区：
文献类型：
--
作者：
Tabb, DL;Huang, YY;Yates, JR
胰蛋白酶消化在蛋白质组学中的主要用途是它在可预测的位置切割蛋白质，但它也因产生以碱性精氨酸和赖氨酸残基终止的肽而值得注意。离子阱串联质谱中的胰蛋白酶肽片段产生显着的 C 末端 y 系列离子。替代的蛋白水解消化可能会产生不遵循这些规则的肽。在这项研究中，我们检查了通过蛋白酶 K 消化产生的 2568 种肽，这种技术可以产生肽中基本残基含量的更多多样性。我们证明肽内碱性残基的位置影响 b 和 y 系列离子的峰强度；肽 N 末端附近的碱性残基可导致显着的 b 系列峰，而不是与胰蛋白酶肽相关的强烈 y 系列峰。分别和组合探讨了精氨酸、赖氨酸和组氨酸的存在和位置的影响。 Arg 显示出最主要的影响，其次是 His，然后是 Lys。含有碱性残基的碎片离子比不含碱性残基的碎片离子产生更强烈的峰。双电荷前体离子通常被建模为仅产生单电荷碎片离子，但包含两个碱性残基的碎片离子可以在碎片过程中接受两个质子。通过表征碱性残基对肽气相断裂的影响，这项研究为肽识别算法提供了更准确的断裂模型。
The primary utility of trypsin digestion in proteomics is that it cleaves proteins at predictable locations, but it is also notable for yielding peptides that terminate in basic arginine and lysine residues. Tryptic peptides fragment in ion trap tandem mass spectrometry to produce prominent C-terminal y series ions. Alternative proteolytic digests may produce peptides that do not follow these rules. In this study, we examine 2568 peptides generated through proteinase K digestion, a technique that produces a greater diversity of basic residue content in peptides. We show that the position of basic residues within peptides influences the peak intensities of b and y series ions; a basic residue near the N-terminus of a peptide can lead to prominent b series peaks rather than the intense y series peaks associated with tryptic peptides. The effects of presence and position for arginine, lysine, and histidine are explored separately and in combination. Arg shows the most dominant effects followed by His and then by Lys. Fragment ions containing basic residues produce more intense peaks than those without basic residues. Doubly charged precursor ions have generally been modeled as producing only singly charged fragment ions, but fragment ions that contain two basic residues may accept both protons during fragmentation. By characterizing the influence of basic residues on gas-phase fragmentation of peptides, this research makes possible more accurate fragmentation models for peptide identification algorithms.