2010年11月12日,，北京生命科學(xué)研究所董夢(mèng)秋實(shí)驗(yàn)室在Journal of Proteome Research雜志發(fā)表題為“Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra”的論文,。
近年來,，電子轉(zhuǎn)移裂解（Electron Transfer Dissociation, ETD ）作為一種新的肽段碎裂方式，在蛋白質(zhì)組學(xué)領(lǐng)域中獲得了廣泛的應(yīng)用,。但是現(xiàn)有的分析軟件不能充分解析ETD質(zhì)譜數(shù)據(jù)，亟待完善,。本文以四十多萬張ETD譜圖為基礎(chǔ),，進(jìn)行了大規(guī)模的統(tǒng)計(jì)分析，系統(tǒng)地總結(jié)了ETD的碎裂規(guī)律與特征,，其中一些是首次發(fā)表,。例如，ETD碎片離子的氫重排（即失去或捕獲一個(gè)甚至多個(gè)氫原子）主要受三種因素的影響：碎片離子類型（c- 或 z- 離子）,、碎片離子相對(duì)于母離子的大小,、以及母離子電荷狀態(tài)，這遠(yuǎn)比以前所認(rèn)識(shí)到的復(fù)雜,。本文將ETD譜圖的特征應(yīng)用到數(shù)據(jù)庫搜索引擎pFind中,，極大地提高了ETD譜圖的鑒定率。在假陽性率為1%的情況下，pFind 從+2價(jià)母離子的ETD譜圖中鑒定到的非冗余肽段數(shù)比Mascot 2.2多63-122%,。對(duì)于更高價(jià)態(tài)的肽段和磷酸化肽段,，pFind也有更好的鑒定結(jié)果。
此研究工作由北京生命科學(xué)研究所董夢(mèng)秋實(shí)驗(yàn)室與中科院計(jì)算所賀思敏教授的pFind課題組共同完成,。pFind課題組副教授孫瑞祥博士是第一作者,。董夢(mèng)秋博士與孫瑞祥博士為共同通訊作者。本文其他作者還有NIBS的宋春青,、楊兵,、陶莉、和景志毅,，以及中科院計(jì)算所遲浩,、秀麗蘊(yùn)、劉超,、王樂珩,、付巖、和賀思敏,。此項(xiàng)目由國家“973”（2010CB912701）,，“863”（2007AA02Z315, 2008AA02Z309, 和2007AA02Z1A7），國家自然科學(xué)基金（30900262）,，中科院知識(shí)創(chuàng)新計(jì)劃（KGGX1-YW-13）,，和北京市政府共同資助完成。（生物谷Bioon.com）
生物谷推薦英文摘要
J. Proteome Res. DOI: 10.1021/pr100648r
Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra
Rui-Xiang Sun*?, Meng-Qiu Dong*?, Chun-Qing Song?, Hao Chi?, Bing Yang?, Li-Yun Xiu?, Li Tao?, Zhi-Yi Jing?, Chao Liu?, Le-Heng Wang?, Yan Fu?, and Si-Min He
Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China, and National Institute of Biological Sciences, Beijing 102206, China
In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis of intact proteins. However, peptide identification rates from ETD spectra compare poorly with those from collision induced dissociation (CID) spectra, especially for doubly charged precursors. This is in part due to an insufficient understanding of the characteristics of ETD and consequently a failure of database search engines to make use of the rich information contained in the ETD spectra. In this study, we statistically characterized ETD fragmentation patterns from a collection of 461440 spectra and subsequently implemented our findings into pFind, a database search engine developed earlier for CID data. From ETD spectra of doubly charged precursors, pFind 2.1 identified 63?122% more unique peptides than Mascot 2.2 under the same 1% false discovery rate. For higher charged peptides as well as phosphopeptides, pFind 2.1 also consistently obtained more identifications. Of the features built into pFind 2.1, the following two greatly enhanced its performance: (1) refined automatic detection and removal of high-intensity peaks belonging to the precursor, charge-reduced precursor, or related neutral loss species, whose presence often set spectral matching askew; (2) a thorough consideration of hydrogen-rearranged fragment ions such as z + H and c ? H for peptide precursors of different charge states. Our study has revealed that different charge states of precursors result in different hydrogen rearrangement patterns. For a fragment ion, its propensity of gaining or losing a hydrogen depends on (1) the ion type (c or z) and (2) the size of the fragment relative to the precursor, and both dependencies are affected by (3) the charge state of the precursor. In addition, we discovered ETD characteristics that are unique for certain types of amino acids (AAs), such as a prominent neutral loss of SCH2CONH2 (90.0014 Da) from z ions with a carbamidomethylated cysteine at the N-terminus and a neutral loss of histidine side chain C4N2H5 (81.0453 Da) from precursor ions containing histidine. The comprehensive list of ETD characteristics summarized in this paper should be valuable for automated database search, de novo peptide sequencing, and manual spectral validation.
