N-连接完整糖肽的质谱分析策略和研究方法

蛋白质糖基化作为最普遍、最重要的蛋白质修饰,一直是组学研究的焦点之一.近十几年来,N-连接糖蛋白质组学研究普遍采用的方法是将糖链与所修饰的多肽分开进行分析.该策略虽降低了分析难度,却也丢失了糖链与蛋白质糖基化位点间重要的对应关系信息.近年来,完整糖肽的质谱分析策略和方法逐步建立起来.总体而言,要实现对完整糖肽的直接质谱分析,首先需要从复杂样品中富集完整糖肽以消除非糖基化多肽对完整糖肽分析的影响,然后在质谱分析中还需要根据糖肽特性调整相应质谱分析参数,最后在后续数据分析中还需要开发相应的分析软件以完成完整糖肽中多肽序列和糖链组成或结构的鉴定.本文即从以上三个主要方面系统阐述目前N-完整糖肽分析中常用的质谱和数据分析策略和方法,并进一步在糖肽谱图识别、母离子单同位素分子质量校正、数据库选择以及假阳性率评估和控制等方面都进行了逐一探讨.完整糖肽的直接质谱分析有助于获取糖链和糖基化位点间的对应关系信息,可为生物标志物发现和疾病致病机理等研究提供更有力的糖蛋白质组学研究工具.     

综述: N-连接完整糖肽的质谱分析策略和研究方法

蛋白质糖基化作为最普遍、最重要的蛋白质修饰，一直是组学研究的焦点之一．近十几年来，N-连接糖蛋白质组学研究普遍采用的方法是将糖链与所修饰的多肽分开进行分析．该策略虽降低了分析难度，却也丢失了糖链与蛋白质糖基化位点间重要的对应关系信息．近年来，完整糖肽的质谱分析策略和方法逐步建立起来．总体而言，要实现对完整糖肽的直接质谱分析，首先需要从复杂样品中富集完整糖肽以消除非糖基化多肽对完整糖肽分析的影响，然后在质谱分析中还需要根据糖肽特性调整相应质谱分析参数，最后在后续数据分析中还需要开发相应的分析软件以完成完整糖肽中多肽序列和糖链组成或结构的鉴定．本文即从以上三个主要方面系统阐述目前N-完整糖肽分析中常用的质谱和数据分析策略和方法，并进一步在糖肽谱图识别、母离子单同位素分子质量校正、数据库选择以及假阳性率评估和控制等方面都进行了逐一探讨．完整糖肽的直接质谱分析有助于获取糖链和糖基化位点间的对应关系信息，可为生物标志物发现和疾病致病机理等研究提供更有力的糖蛋白质组学研究工具．     

N-糖基化位点鉴定方法和非经典N-糖基化序列

蛋白质的N-糖基化修饰是生物体调控蛋白质在组织和细胞中的定位、功能、活性、寿命和多样性的一种普遍的翻译后方式。N-糖基化位点是理解糖链功能的重要前提之一。应用新的糖蛋白、糖肽富集技术和质谱技术,科学家们在不同组织中完成了对N-糖基化位点的鉴定。此外,不同于经典三联子的N-糖基化序列的发现使人们对N-糖基化过程的认识向纵深发展。     

基于超滤膜辅助的糖蛋白全N-连接糖链的富集和质谱解析

糖基化作为一种常见的蛋白质翻译后修饰,对蛋白质的空间结构、生物功能等具有重要的影响.解析糖蛋白糖链结构有助于更清楚地认识糖蛋白及其功能.本研究建立了一种基于超滤膜富集血清中糖蛋白全N-连接糖链,并利用质谱技术对糖链结构进行分析的方法.根据糖蛋白及其糖链结构之间的分子质量差异,利用Millipore公司的10 ku超滤膜富集血清糖蛋白上酶解(PNGase F)释放的全N-连接糖链,并使用MALDI-TOF/TOF-MS解析糖链结构.通过该技术可以从血清中富集并鉴定到23种独特的N-连接的糖链结构,并且利用二级质谱进行了结构确认.该方法可以被用于从大量生物样本中富集糖蛋白全N-连接糖链,可以达到快速、高通量地解析糖蛋白N-连接糖链的目的.     

基于电子捕获裂解/电子转运裂解串联质谱技术的蛋白质组学研究

蛋白质组学的兴起带动了质谱技术的快速发展,而质谱技术的进步则拓宽了蛋白质组学研究问题的广度.最近10年内,肽段或完整蛋白质在质谱仪中的裂解技术——电子捕获裂解(electron capture dissociation,ECD)与电子转运裂解(electron transfer dissociation,ETD)逐渐发展起来.ECD和ETD在蛋白质组学中的应用,特别是在蛋白质的翻译后修饰鉴定和自顶而下(Top-down)的完整蛋白质裂解研究中已经展示出了诱人的前景.对ECD和ETD的基本原理、质谱特点、仪器实现、数据解析算法与软件开发,以及在蛋白质组学中的应用进展等方面进行了比较系统全面的阐述,并对当前的研究问题、面临的技术挑战与未来的发展趋势等方面作了深入剖析.     

基于生物质谱的蛋白质O-GalNAc糖基化修饰研究进展

糖基化是生物体内蛋白质最常见、最重要的翻译后修饰之一,普遍存在于细胞膜蛋白及分泌蛋白,执行重要的生物学功能.常见的蛋白糖基化修饰有N-糖基化及O-糖基化两种类型,而O-GalNAc是O-糖基化中重要的存在形式,在特定生物学进程、癌症发生发展中起着重要作用,近年来受到广泛重视.得益于代谢标记、化学衍生化、高分辨和多种碎裂模式质谱技术以及基因编辑技术的高速发展,O-GalNAc的糖基化位点、糖型鉴定和生理功能研究取得一系列重大进展.本文综述了基于生物质谱技术的蛋白质O-GalNAc糖基化修饰研究进展.     

糖基化蛋白质组学:结构、功能和研究方法

蛋白质糖基化修饰结构多样、分布广泛,以N-糖基化、O-Gal NAc糖基化和O-Glc NAc糖基化等不同修饰形式存在。糖修饰以各种方式广泛参与基本生物学过程,包括基因转录、蛋白质翻译、信号转导、细胞-细胞间以及宿主-病原体相互作用等。糖基化修饰的异常变化与多种重要疾病的发生发展相关,包括免疫性疾病、肿瘤、先天性糖缺陷等。该文系统展示几种常见糖修饰的结构、参与的生理病理过程,以及最新的研究方法,尤其是糖修饰蛋白质或肽段的特异性富集方法和基于质谱的序列分析方法进展,以期丰富糖修饰蛋白质的研究手段,为糖蛋白质功能机制研究、疾病治疗靶标或候选标志物的发现提供新视角。     

植物N-糖链检测技术研究进展

N-糖基化作为一种重要的蛋白质翻译后修饰,在胚胎发育、癌症发生发展及免疫防御等诸多复杂的生命活动中发挥着关键作用。近年来,基于质谱的N-糖链的检测及其定量研究在动物方面取得了显著进展,相比之下,植物N-糖基化及N-糖链检测的相关研究要远远滞后,这也是制约植物糖生物学研究发展的关键瓶颈问题之一。对蛋白质N-糖链的释放、定量策略、可视化检测及其在植物中的应用进展进行了归纳总结,以期为指导后续植物N-糖链及N-糖组的定性定量检测提供参考。     

凝集素法与酰肼法富集糖肽的方法学比较

蛋白质糖基化(glycosylation)是最常见和最重要的翻译后修饰之一.大规模N-连接糖基化位点鉴定是糖蛋白质组学研究的重要组成部分,而N-连接糖肽富集是高通量N-连接糖基化位点鉴定的关键步骤.凝集素富集法和酰肼化学法是目前被广泛应用的N-连接糖肽富集技术,有报道认为两种方法具有很强的互补性,联合使用能提高糖基化位点的鉴定数目.本文以Hep G2细胞系为模型,系统比较了这两种方法的富集效率和糖蛋白鉴定数目.结果表明,虽然酰肼法的糖肽富集效率为76.6%,远高于凝集素法的54.6%,但是凝集素法却能鉴定到825个糖蛋白和1 959个N-连接糖基化位点,显著多于酰肼法富集到的522个糖蛋白和1 014个糖基化位点.并且,两种方法并未显示出显著的互补性,仅28个糖蛋白和80个糖基化位点未在凝集素法中鉴定到.     

蛋白质糖基化分析方法及其在蛋白质组学中的应用

作为一种普遍存在的翻译后修饰,糖基化对蛋白质的结构和功能有着重要影响。弄清糖基化发生发展的规律是理解蛋白质复杂多样的生物功能的一个重要前提。糖基化发生的特点决定了糖基化相关研究是对分析技术的一大挑战。作为蛋白质组学研究的重要组成部分,目前蛋白质糖基化研究的重点和难点主要集中于糖蛋白／糖肽的分离富集和糖蛋白的鉴定／糖基化位点的确定2个方面,相关技术已用于蛋白质组学水平的糖基化研究,但都还不够成熟。以生物质谱为核心、多学科交叉的蛋白质组学技术始终处于不断发展之中。基于糖基化发生规律的富集检测技术的发展、移动质子理论的提出及电子捕获裂解技术的应用必将极大地促进包括糖基化在内的翻译后修饰研究。蛋白质糖基化的研究有助于从基因组-蛋白组-糖组这样一个宏观的综合的水平观察分析生命现象,从而达到对生命现象更本质的认识。     

Peptide identification by tandem mass spectrometry with alternate fragmentation modes

The high-throughput nature of proteomics mass spectrometry is enabled by a productive combination of data acquisition protocols and the computational tools used to interpret the resulting spectra. One of the key components in mainstream protocols is the generation of tandem mass (MS/MS) spectra by peptide fragmentation using collision induced dissociation, the approach currently used in the large majority of proteomics experiments to routinely identify hundreds to thousands of proteins from single mass spectrometry runs. Complementary to these, alternative peptide fragmentation methods such as electron capture/transfer dissociation and higher-energy collision dissociation have consistently achieved significant improvements in the identification of certain classes of peptides, proteins, and post-translational modifications. Recognizing these advantages, mass spectrometry instruments now conveniently support fine-tuned methods that automatically alternate between peptide fragmentation modes for either different types of peptides or for acquisition of multiple MS/MS spectra from each peptide. But although these developments have the potential to substantially improve peptide identification, their routine application requires corresponding adjustments to the software tools and procedures used for automated downstream processing. This review discusses the computational implications of alternative and alternate modes of MS/MS peptide fragmentation and addresses some practical aspects of using such protocols for identification of peptides and post-translational modifications.     

Electron Capture Dissociation Mass Spectrometry in Characterization of Peptides and Proteins

Electron capture dissociation (ECD) represents one of the most recent and significant advancements in tandem mass spectrometry (MS/MS) for the identification and characterization of polypeptides. In comparison with the conventional fragmentation techniques, such as collisionally activated dissociation (CAD), ECD provides more extensive sequence fragments, while allowing the labile modifications to remain intact during backbone fragmentation—an important attribute for characterizing post-translational modifications. Herein, we present a brief overview of the ECD technique as well as selected applications in characterization of peptides and proteins. Case studies including characterization and localization of amino acid glycosylation, methionine oxidation, acylation, and “top–down” protein mass spectrometry using ECD will be presented. A recent technique, coined as electron transfer dissociation (ETD), will be also discussed briefly.     

The utility of ETD mass spectrometry in proteomic analysis

Mass spectrometry has played an integral role in the identification of proteins and their post-translational modifications (PTM). However, analysis of some PTMs, such as phosphorylation, sulfonation, and glycosylation, is difficult with collision-activated dissociation (CAD) since the modification is labile and preferentially lost over peptide backbone fragmentation, resulting in little to no peptide sequence information. The presence of multiple basic residues also makes peptides exceptionally difficult to sequence by conventional CAD mass spectrometry. Here we review the utility of electron transfer dissociation (ETD) mass spectrometry for sequence analysis of post-translationally modified and/or highly basic peptides. Phosphorylated, sulfonated, glycosylated, nitrosylated, disulfide bonded, methylated, acetylated, and highly basic peptides have been analyzed by CAD and ETD mass spectrometry. CAD fragmentation typically produced spectra showing limited peptide backbone fragmentation. However, when these peptides were fragmented using ETD, peptide backbone fragmentation produced a complete or almost complete series of ions and thus extensive peptide sequence information. In addition, labile PTMs remained intact. These examples illustrate the utility of ETD as an advantageous tool in proteomic research by readily identifying peptides resistant to analysis by CAD. A further benefit is the ability to analyze larger, non-tryptic peptides, allowing for the detection of multiple PTMs within the context of one another.     

A review of methods for interpretation of glycopeptide tandem mass spectral data

Despite the publication of several software tools for analysis of glycopeptide tandem mass spectra, there remains a lack of consensus regarding the most effective and appropriate methods. In part, this reflects problems with applying standard methods for proteomics database searching and false discovery rate calculation. While the analysis of small post-translational modifications (PTMs) may be regarded as an extension of proteomics database searching, glycosylation requires specialized approaches. This is because glycans are large and heterogeneous by nature, causing glycopeptides to exist as multiple glycosylated variants. Thus, the mass of the peptide cannot be calculated directly from that of the intact glycopeptide. In addition, the chemical nature of the glycan strongly influences product ion patterns observed for glycopeptides. As a result, glycopeptidomics requires specialized bioinformatics methods. We summarize the recent progress towards a consensus for effective glycopeptide tandem mass spectrometric analysis.     

Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry

The enormous complexity, wide dynamic range of relative protein abundances of interest (over 10 orders of magnitude), and tremendous heterogeneity (due to post-translational modifications, such as glycosylation) of the human blood plasma proteome severely challenge the capabilities of existing analytical methodologies. Here, we describe an approach for broad analysis of human plasma N-glycoproteins using a combination of immunoaffinity subtraction and glycoprotein capture to reduce both the protein concentration range and the overall sample complexity. Six high-abundance plasma proteins were simultaneously removed using a pre-packed, immobilized antibody column. N-linked glycoproteins were then captured from the depleted plasma using hydrazide resin and enzymatically digested, and the bound N-linked glycopeptides were released using peptide-N-glycosidase F (PNGase F). Following strong cation exchange (SCX) fractionation, the deglycosylated peptides were analyzed by reversed-phase capillary liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Using stringent criteria, a total of 2053 different N-glycopeptides were confidently identified, covering 303 nonredundant N-glycoproteins. This enrichment strategy significantly improved detection and enabled identification of a number of low-abundance proteins, exemplified by interleukin-1 receptor antagonist protein (approximately 200 pg/mL), cathepsin L (approximately 1 ng/mL), and transforming growth factor beta 1 (approximately 2 ng/mL). A total of 639 N-glycosylation sites were identified, and the overall high accuracy of these glycosylation site assignments as assessed by accurate mass measurement using high-resolution liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) is initially demonstrated.     

Intact glycopeptide characterization using mass spectrometry

Glycosylation is one of the most prominent and extensively studied protein post-translational modifications. However, traditional proteomic studies at the peptide level (bottom-up) rarely characterize intact glycopeptides (glycosylated peptides without removing glycans), so no glycoprotein heterogeneity information is retained. Intact glycopeptide characterization, on the other hand, provides opportunities to simultaneously elucidate the glycan structure and the glycosylation site needed to reveal the actual biological function of protein glycosylation. Recently, significant improvements have been made in the characterization of intact glycopeptides, ranging from enrichment and separation, mass spectroscopy (MS) detection, to bioinformatics analysis. In this review, we recapitulated currently available intact glycopeptide characterization methods with respect to their advantages and limitations as well as their potential applications.     

Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins.     

Determination of aberrant O-glycosylation in the IgA1 hinge region by electron capture dissociation fourier transform-ion cyclotron resonance mass spectrometry

In a number of human diseases of chronic inflammatory or autoimmune character, immunoglobulin molecules display aberrant glycosylation patterns of N- or O-linked glycans. In IgA nephropathy, IgA1 molecules with incompletely galactosylated O-linked glycans in the hinge region (HR) are present in mesangial immunodeposits and in circulating immune complexes. It is not known whether the Gal deficiency in IgA1 proteins occurs randomly or preferentially at specific sites. To develop experimental approaches to address this question, the synthetic IgA1 hinge region and hinge region from a naturally Gal-deficient IgA1 myeloma protein have been analyzed by 9.4 tesla Fourier transform-ion cyclotron resonance mass spectrometry. Fourier transform-ion cyclotron resonance mass spectrometry offers two complementary fragmentation techniques for analysis of protein glycosylation by tandem mass spectrometry. Infrared multiphoton dissociation of isolated myeloma IgA1 hinge region peptides confirms the amino acid sequence of the de-glycosylated peptide and positively identifies a series of fragments differing in O-glycosylation. To localize sites of O-glycan attachment, synthetic IgA1 HR glycopeptides and HR from a naturally Gal-deficient polymeric IgA1 myeloma protein were analyzed by electron capture dissociation and activated ion-electron capture dissociation. Multiple sites of O-glycan attachment (including sites of Gal deficiency) in myeloma IgA1 HR glycoforms were identified (in all but one case uniquely). These results represent the first direct identification of multiple sites of O-glycan attachment in IgA1 hinge region by mass spectrometry, thereby enabling future characterization at the molecular level of aberrant glycosylation of IgA1 in diseases such as IgA nephropathy.