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        定量蛋白質(zhì)組學(xué)質(zhì)譜采集技術(shù)進(jìn)展

        2014-12-18 21:24:52張偉
        分析化學(xué) 2014年12期
        關(guān)鍵詞:綜述

        張偉

        摘 要 質(zhì)譜是定量蛋白組學(xué)的主要工具。近年來(lái)隨著定量蛋白質(zhì)組學(xué)研究的深入,傳統(tǒng)質(zhì)譜定量技術(shù)面臨著復(fù)雜基質(zhì)干擾、分析通量限制等諸多問(wèn)題。而最近一系列質(zhì)譜新技術(shù)的發(fā)展,包括同步母離子選擇(SPS)、質(zhì)量虧損標(biāo)記、平行反應(yīng)監(jiān)測(cè)(PRM)、多重累積(MSX)和多種全新數(shù)據(jù)非依賴性采集(DIA)等,為解決目前蛋白質(zhì)組學(xué)在相對(duì)定量和絕對(duì)定量分析方面的局限提供了有效途徑。本文對(duì)定量蛋白質(zhì)組學(xué)目前遇到的瓶頸問(wèn)題進(jìn)行了分析,總結(jié)了質(zhì)譜定量采集技術(shù)的最新進(jìn)展,并評(píng)述了這些新技術(shù)的特點(diǎn)以及在定量蛋白質(zhì)組學(xué)應(yīng)用中的優(yōu)勢(shì)。

        [KH*3/4D][HTH]關(guān)鍵詞 [HTSS]定量蛋白質(zhì)組學(xué); 同步母離子選擇; 平行反應(yīng)監(jiān)測(cè); 數(shù)據(jù)非依賴性采集; 綜述

        [HT][HK][FQ(32,X,DY-W] [CD15] 20140910收稿; 20141018接受

        * Email: wei.zhang@thermofisher.com [HT]

        1 引 言

        當(dāng)今蛋白質(zhì)組學(xué)的關(guān)注焦點(diǎn)和研究趨勢(shì)已經(jīng)逐漸從定性分析 轉(zhuǎn)向定量分析。定量蛋白質(zhì)組學(xué)是對(duì)細(xì)胞、組織乃至完整生物體的蛋白質(zhì)表達(dá)進(jìn)行定量分析,對(duì)生物過(guò)程機(jī)理的探索和臨床診斷標(biāo)志物的發(fā)現(xiàn)與驗(yàn)證具有重要意義[ 1,2]。定量蛋白質(zhì)組學(xué)分為相對(duì)定量與絕對(duì)定量[ 3]。相對(duì)定量即差異比較,通過(guò)質(zhì)譜大規(guī)模、高通量地對(duì)兩種或多種不同生理、病理?xiàng)l件下的樣本進(jìn)行定量分析,獲得蛋白質(zhì)表達(dá)量的精確差異, 主要方法有穩(wěn)定同位素標(biāo)記和非標(biāo)記兩種技術(shù)手段[ 4,5]。絕對(duì)定量即獲得蛋白的具體表達(dá)量,利用質(zhì)譜監(jiān)測(cè)目標(biāo)蛋白的專(zhuān)一性肽段(Unique Peptide)獲得色譜質(zhì)譜峰面積,并與已知量的標(biāo)準(zhǔn)肽段(外標(biāo)法)或穩(wěn)定同位素標(biāo)記的重標(biāo)肽段(內(nèi)標(biāo)法)比較確定具體量,實(shí)現(xiàn)絕對(duì)定量。主要質(zhì)譜方法是對(duì)專(zhuān)一性肽段進(jìn)行選擇反應(yīng)監(jiān)測(cè)或稱(chēng)多反應(yīng)監(jiān)測(cè)(Selected/Multiple reaction monitoring, SRM/MRM)[ 6]。

        穩(wěn)定同位素標(biāo)記技術(shù)是蛋白質(zhì)組學(xué)相對(duì)定量的經(jīng)典方法。樣本在穩(wěn)定同位素標(biāo)記后、質(zhì)譜分析前混合,一次分析實(shí)現(xiàn)差異定量,有效消除了色譜和質(zhì)譜分離分析過(guò)程中的不穩(wěn)定性,最大程度減小了定量誤差。常見(jiàn)方法有基于代謝標(biāo)記的SILAC[ 7]、基于酶解標(biāo)記的18O標(biāo)記[ 8]和基于化學(xué)標(biāo)記的二甲基化[ 9]等,這些方法通過(guò)一級(jí)母離子提取峰面積實(shí)現(xiàn)定量比較。但是,一級(jí)定量具有標(biāo)記通量低、動(dòng)態(tài)范圍差、靈敏度不高等不足,因此, 近年來(lái),基于同重同位素標(biāo)記的二級(jí)定量方法使用越來(lái)越廣泛[ 10]。利用同重同位素標(biāo)簽標(biāo)記肽段,在一級(jí)質(zhì)譜不同樣本的肽段分子量沒(méi)有區(qū)分,相互疊加,提高了靈敏度; 二級(jí)碎裂獲得分子量不同的報(bào)告離子,在b/y離子定性的同時(shí),通過(guò)報(bào)告離子之間的強(qiáng)度差異實(shí)現(xiàn)定量,提高了動(dòng)態(tài)范圍。同重同位素主要標(biāo)記試劑有iTRAQ[ 11]和TMT[ 12],標(biāo)簽容量分別達(dá)到了8標(biāo)和6標(biāo)。然而,同重同位素標(biāo)記技術(shù)面臨共洗脫肽段干擾的問(wèn)題。蛋白質(zhì)組學(xué)樣本非常復(fù)雜,在色譜上存在大量共洗脫肽段,而質(zhì)譜在選擇母離子進(jìn)行二級(jí)分析時(shí),選擇窗口通常在m/z 2左右,分子量接近的共洗脫肽段被同時(shí)選擇,碎裂出的報(bào)告離子與目標(biāo)肽段報(bào)告離子疊加,降低了定量比例的準(zhǔn)確性[ 13,14]。Ting等[ 15]研究證明,在復(fù)雜樣本中,共洗脫肽段嚴(yán)重干擾了報(bào)告離子的強(qiáng)度,造成肽段和蛋白的定量比例低于真實(shí)比例,產(chǎn)生“低估效應(yīng)”。這一問(wèn)題已成為同重同位素標(biāo)記定量技術(shù)的瓶頸。

        基于三重四極桿的SRM(或稱(chēng)MRM)是質(zhì)譜定量的金標(biāo)準(zhǔn),在蛋白質(zhì)絕對(duì)定量中也廣泛使用[ 6]。SRM根據(jù)專(zhuān)一性肽段的母離子質(zhì)量和子離子質(zhì)量,第一級(jí)質(zhì)量分析器(Q1)篩選母離子,進(jìn)入碰撞池碎裂后,第二級(jí)質(zhì)量分析器(Q3)再篩選子離子,最大程度地去除干擾離子,監(jiān)測(cè)母離子子離子形成的離子對(duì)的信號(hào)響應(yīng)。通過(guò)外標(biāo)法,利用已知量的標(biāo)準(zhǔn)肽段繪制標(biāo)準(zhǔn)曲線; 或內(nèi)標(biāo)法,直接加入已知量的同位素重標(biāo)肽段同時(shí)監(jiān)測(cè),從而實(shí)現(xiàn)定性確證和定量檢測(cè)[ 6,16]。SRM靈敏度高、線性范圍廣,是目標(biāo)蛋白驗(yàn)證和絕對(duì)定量的有效手段。然而,隨著定量蛋白質(zhì)組學(xué)的深入發(fā)展,樣本基質(zhì)越來(lái)越復(fù)雜、目標(biāo)蛋白豐度越來(lái)越低,容易受到高豐度蛋白的掩蓋。而SRM由于質(zhì)量分辨率低,難以有效去除復(fù)雜基質(zhì)背景的干擾,易造成假陽(yáng)性[ 17,18]。另一方面,隨著分析通量的要求越來(lái)越高,一次分析可能需要監(jiān)測(cè)成千上萬(wàn)個(gè)離子對(duì),而SRM速度和靈敏度的局限使得能同時(shí)監(jiān)測(cè)的離子對(duì)數(shù)量有限[ 19]; 此外,離子對(duì)、碰撞能量等條件的優(yōu)化也費(fèi)時(shí)費(fèi)力,難以滿足目標(biāo)蛋白質(zhì)組學(xué)高通量發(fā)展的需要,特別是大樣本量的生物標(biāo)志物和系統(tǒng)生物學(xué)研究[ 20,21]。因此,蛋白質(zhì)絕對(duì)定量同樣面臨著較大的技術(shù)挑戰(zhàn)。

        近兩年來(lái),隨著以O(shè)rbitrap為代表的高分辨質(zhì)譜硬件技術(shù)不斷進(jìn)步、采集方法不斷創(chuàng)新,定量蛋白質(zhì)組學(xué)遇到的諸多瓶頸正逐步得到解決。這些技術(shù)包括基于同重同位素標(biāo)記技術(shù)的同步母離子選擇和質(zhì)量虧損標(biāo)記,相對(duì)于傳統(tǒng)SRM掃描的高分辨平行反應(yīng)監(jiān)測(cè)和多重累積平行反應(yīng)監(jiān)測(cè),以及多種全新數(shù)據(jù)非依賴性采集技術(shù)。

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        Progress in Mass Spectrometry Acquisition Approach for

        Quantitative Proteomics

        ZHANG Wei*

        (Thermo Fisher Scientific, Shanghai 201206, China)

        Abstract Mass spectrometry is an important and powerful tool for protein quantification. With the indepth development of quantitative proteomics, limitations of classic MS based quantification methods, such as complicated matrix interference and throughput/capacity limitation, start to appear. Recent progress of series novel MS based techniques provide effective solutions for the limitations of relative and absolute proteomic quantification, including synchronous precursor selection (SPS), mass defect isobaric labeling, parallel reaction monitoring (PRM), multiplexing acquisition (MSX), and various novel data independent acquisition (DIA) modes. Here we summarized the current limitations of quantitative proteomics, reviewed the latest MS based quantification approaches, and discussed the features and advantages of these novel techniques for quantitative proteomic application.

        Keywords Quantitative proteomics; Synchronous precursor selection; Parallel reaction monitoring; Data independent acquisition; Review

        (Received 10 September 2014; accepted 18 October 2014)

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        54 Egertson J D, Kuehn A, Merrihew G E, Bateman N W, MacLean B X, Ting Y S, Canterbury J D, Marsh D M, Kellmann M, Zabrouskov V, Wu C C, MacCoss M J. Nat. Methods, 2013, 10(8): 744-746

        55 Senko M W, Remes P M, Canterbury J D, Mathur R, Song Q, Eliuk S M, Mullen C, Earley L, Hardman M, Blethrow JD, Bui H, Specht A, Lange O, Denisov E, Makarov A, Horning S, Zabrouskov V. Anal. Chem., 2013, 85(24): 11710-11714

        56 Kiyonami R, Patel B, Senko M, Zabrouskov V, Egertson J, Ting S, MacCoss M, Rogers J, Huhmer A. Large Scale Targeted Protein Quantification Using WiSIMDIA Workflow on a Orbitrap Fusion Tribrid Mass Spectrometer. ASMS, 2014, W737

        57 ZHANG Wei, Reiko Kiyonami, JIANG Zheng, CHEN Wei. Chinese J. Anal. Chem., 2014, 42(12): 1750-1758

        張 偉, Reiko Kiyonami, 江 崢, 陳 偉. 分析化學(xué), 2014, 42(12): 1750-1758

        58 Prakash A, Peterman S, Ahmad S, Sarracino D, Frewen B, Vogelsang M, Byram G, Krastins B, Vadali G, Lopez M. J. Proteome Res., 2014, doi: 10.1021/pr5003017

        Progress in Mass Spectrometry Acquisition Approach for

        Quantitative Proteomics

        ZHANG Wei*

        (Thermo Fisher Scientific, Shanghai 201206, China)

        Abstract Mass spectrometry is an important and powerful tool for protein quantification. With the indepth development of quantitative proteomics, limitations of classic MS based quantification methods, such as complicated matrix interference and throughput/capacity limitation, start to appear. Recent progress of series novel MS based techniques provide effective solutions for the limitations of relative and absolute proteomic quantification, including synchronous precursor selection (SPS), mass defect isobaric labeling, parallel reaction monitoring (PRM), multiplexing acquisition (MSX), and various novel data independent acquisition (DIA) modes. Here we summarized the current limitations of quantitative proteomics, reviewed the latest MS based quantification approaches, and discussed the features and advantages of these novel techniques for quantitative proteomic application.

        Keywords Quantitative proteomics; Synchronous precursor selection; Parallel reaction monitoring; Data independent acquisition; Review

        (Received 10 September 2014; accepted 18 October 2014)

        46 Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Mol. Cell. Proteomics, 2012, 11(12): 1709-1723

        47 Law K P, Lim Y P. Expert. Rev. Proteomics, 2013, 10(6): 551-566

        48 Venable J D, Dong M Q, Wohlschlegel J, Dillin A, Yates J R. Nat. Methods, 2004, 1(1): 39-45

        49 Gillet L C, Navarro P, Tate S, Rost H, Selevsek N, Reiter L, Bonner R, Aebersold R. Mol. Cell. Proteomics, 2012, 11(6): O111.016717

        50 Liu Y, Huttenhain R, Surinova S, Gillet L C, Mouritsen J, Brunner R, Navarro P, Aebersold R. Proteomics, 2013, 13(8): 1247-1256

        51 Collins B C, Gillet L C, Rosenberger G, Rost H L, Vichalkovski A, Gstaiger M, Aebersold R. Nat. Methods, 2013, 10(12): 1246-1253

        52 Lambert J P, Ivosev G, Couzens A L, Larsen B, Taipale M, Lin Z Y, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras A C. Nat. Methods, 2013, 10(12): 1239-1245

        53 Chapman J D, Goodlett D R, Masselon C D. Mass Spectrom. Rev., 2013: 10.1002/mas.21400

        54 Egertson J D, Kuehn A, Merrihew G E, Bateman N W, MacLean B X, Ting Y S, Canterbury J D, Marsh D M, Kellmann M, Zabrouskov V, Wu C C, MacCoss M J. Nat. Methods, 2013, 10(8): 744-746

        55 Senko M W, Remes P M, Canterbury J D, Mathur R, Song Q, Eliuk S M, Mullen C, Earley L, Hardman M, Blethrow JD, Bui H, Specht A, Lange O, Denisov E, Makarov A, Horning S, Zabrouskov V. Anal. Chem., 2013, 85(24): 11710-11714

        56 Kiyonami R, Patel B, Senko M, Zabrouskov V, Egertson J, Ting S, MacCoss M, Rogers J, Huhmer A. Large Scale Targeted Protein Quantification Using WiSIMDIA Workflow on a Orbitrap Fusion Tribrid Mass Spectrometer. ASMS, 2014, W737

        57 ZHANG Wei, Reiko Kiyonami, JIANG Zheng, CHEN Wei. Chinese J. Anal. Chem., 2014, 42(12): 1750-1758

        張 偉, Reiko Kiyonami, 江 崢, 陳 偉. 分析化學(xué), 2014, 42(12): 1750-1758

        58 Prakash A, Peterman S, Ahmad S, Sarracino D, Frewen B, Vogelsang M, Byram G, Krastins B, Vadali G, Lopez M. J. Proteome Res., 2014, doi: 10.1021/pr5003017

        Progress in Mass Spectrometry Acquisition Approach for

        Quantitative Proteomics

        ZHANG Wei*

        (Thermo Fisher Scientific, Shanghai 201206, China)

        Abstract Mass spectrometry is an important and powerful tool for protein quantification. With the indepth development of quantitative proteomics, limitations of classic MS based quantification methods, such as complicated matrix interference and throughput/capacity limitation, start to appear. Recent progress of series novel MS based techniques provide effective solutions for the limitations of relative and absolute proteomic quantification, including synchronous precursor selection (SPS), mass defect isobaric labeling, parallel reaction monitoring (PRM), multiplexing acquisition (MSX), and various novel data independent acquisition (DIA) modes. Here we summarized the current limitations of quantitative proteomics, reviewed the latest MS based quantification approaches, and discussed the features and advantages of these novel techniques for quantitative proteomic application.

        Keywords Quantitative proteomics; Synchronous precursor selection; Parallel reaction monitoring; Data independent acquisition; Review

        (Received 10 September 2014; accepted 18 October 2014)

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