电子捕获解离技术在生物质谱中的作用

电子捕获解离(ECD)是一种非各态历经的(non-ergodic)解离方式,可导致多肽中N-C_α键断裂,也能更优先断裂S-S键,在较高电子能量条件下还可以区分亮氨酸和异亮氨酸,并且在断裂过程中能完整保留蛋白质分子的修饰位点。因此,它与碰撞活化解离(CAD)等传统解离方式形成了较为理想的互补。ECD与CAD的联合使用可提供更广泛的多肽覆盖率序列信息,提高蛋白测序的效率与准确度。本文在介绍ECD基本原理、解离机理的基础上,简要地总结了ECD技术在生物质谱中的作用。     

多肽植物激素系统素及相似多肽的质谱裂解机理和反相色谱保留规律研究

采用液相色谱-四级杆飞行时间质谱(LC-QTOF-MS)联用技术,研究了系统素及其相似多肽的质谱裂解机理和色谱保留规律,探讨了它们的碰撞诱导解离规律.结果表明,系统素准分子离子一般带有2-5个电荷;在低碰撞能条件下,多肽母离子发生碰撞诱导解离,产生b型和Y型碎片离子;烟草系统素I最强母离子[M+3H]3+的最优碰撞能为...     

精氨酸残基在质子化多肽RRMKWKK的气相碰撞诱导解离过程中的作用

用ESI/MS-MS方法研究了质子化多肽RRMKWKK 在低能气相碰撞诱导解离(CID)条件下的碰撞能和解离路径. 研究结果表明, [M+2H]2+和[M+3H]3+的CID断裂曲线和断裂位点相似. 但质子化多肽所含正电荷个数不同时, 产生同一碎片离子的初始碰撞能不同. 碱性氨基酸残基精氨酸(Arg)的支链是多肽RRMKWKK质子化时质子优先结合的位点, 导致含有Arg的多肽在气相碰撞诱导解离条件下解离时需要较高的碰撞能. 在用质谱方法研究含精氨酸残基的多肽时应选择质子个数比多肽中Arg个数多1个的母体离子. 质子化多肽RRMKWKK的结构AM1计算结果表明, 质子化RRMKWKK中两个相邻精氨酸在空间上相互分离, 库伦斥力的影响不足以改变质子的优先结合位点.     

C_nSH~±与C_nS_2~±的碰撞诱导解离研究

在自制的交叉分子-离子束串级飞行时间质谱仪上，以激光溅射的方式，产生了一系列含有一个硫原子和一个氢原子与含有两个硫原子的杂碳原子簇正负离子、经“质量门”选出单一质量的簇离子，与氮气的超声分子束交叉碰撞，然后分析其碰撞碎片．研究结果确定了这些簇离子的结构，两个杂原子分别位于碳链的两端．对碎片离子的分析还揭示了这些簇离子的主要解离通道及其与成簇碳原子数和所带电荷极性的关系，发现当成簇碳原子数较少时，簇离子中最薄弱的是S－C键，随着残链的增长，与硫原子相邻的C－C键变得更为薄弱；实验中存在着多次碰撞的机会，因而各碎片离子还有可能进一步解离．     

原子簇离子解离统计分布的动力学研究

对激光产生的原子簇离子，通过质量选择，可以对选出的原子簇离子进行碰撞诱导解离或光解离研究，在对实验记录的解离质谱的分析中发现，同一系列碎片离子的相丰度分布符合一定的统计规律，不同的统计分布形式对于不同的解离机理，通过求解解离反应的动力学方程，得到碎片离子统计分布的函数表达式，从而可以通过分析解离质谱中碎片中离子的统计分布，探讨相应的原子簇离子解离反应的机理。     

溴甲烷在强激光场中的电离和解离

利用自制的反射式飞行时间质谱仪(RTOF-MS)研究了多原子分子CH₃Br在强激光场中的电离解离. 得到了溴甲烷在强激光场中电离解离的飞行时间质谱, 基于RTOF-MS的高分辨率(M/ΔM>2000), 测量了分子库仑爆炸产生的系列碎片离子的动能释放(KER), 用多光子解离和库仑爆炸解释了实验结果. 与碘甲烷在强场中的实验结果对比发现: (1) 在相同的激光场强下, 碘甲烷电离解离的最高价碎片离子为I⁶⁺而溴甲烷为Br³⁺; (2) 溴甲烷质谱中存在母体离子的脱氢产物CH_mBr⁺ 和CH_mBr²⁺, 而对于碘甲烷, 没有检测到这些通道, C-I键首先断开; (3) 质谱中存在H⁷⁹Br⁺和H⁸¹Br⁺, 而碘甲烷的电离解离中不存在HI产物; (4) 溴甲烷库仑两体爆炸的有效电荷间距随着两碎片电荷乘积的增大而增大, 而对于碘甲烷此间距几乎不随电荷乘积变化; (5) CH_m⁺(m=0, 1, 2)的主要生成通道可能与碘甲烷不同, 不是来自CH₃⁺的顺序脱氢, 而是来自脱氢母体离子的直接解离.     

亲水相互作用色谱结合串联质谱多重碎裂模式在完整糖肽研究中的应用

蛋白质的糖基化修饰在生理及病理过程中发挥着重要作用。由于技术条件的限制,传统的糖蛋白分析方法中,通常分别鉴定蛋白质和糖链两者的结构,而忽略了蛋白质与糖链的连接关系。本研究旨在以完整糖肽作为检测对象,对糖肽中肽段序列和糖链结构的同步解析。采用亲水相互作用色谱对完整糖肽进行分离纯化,联合生物质谱中碰撞诱导解离(CID)、高能诱导解离(HCD)、电子转移解离(ETD)等裂解模式,对完整糖肽的糖基化位点、糖链结构、肽段序列等进行全方面的解析。结果表明,亲水相互作用色谱中样品与填料比1∶50可有效富集糖肽,采用30%CID能量,主要产生糖苷键断裂的碎片,为糖链的结构组成分析提供了线索;采用25%HCD能量,在低分子量区域提供了糖链的特征离子信息,并产生明确的糖肽Y1特征离子;ETD保留了完整的修饰基团而产生肽段骨架的断裂,可以提供有效的肽段序列信息。本研究结合亲水相互作用色谱与质谱仪中的多种碎裂方式,为完整糖肽的结构解析提供了一种快速、有效的研究方案。     

碰撞气体的种类和压力对离子阱质谱性能的影响

基于数字离子阱技术,研究了离子阱质谱分析实验过程使用的碰撞气体种类及压力对离子阱质谱性能,如质量分辨能力、信号强度、串级质谱分析,以及低质量截止效应等的影响.实验过程中,在离子的激发和碰撞诱导解离阶段,分别采用质量数不等的氦气(质量数=4 amu)、氮气(质量数=28 amu)、氩气(质量数=40 amu)等作为碰撞气体,以及不同的气体压力,研究了它们对质谱性能的影响.结果表明,当采用质量数较大的氩气作为碰撞气体时,可以有效改善低质量数截止效应和提高离子碰撞过程中的能量转移效率,同时提高离子捕获和解离效率,但是质量分辨率会明显降低.在获得较高质量分辨率方面,氦气作为碰撞气体时效果最好.在气压相同的情况下,质量数大的碰撞气体有利于提高串级质谱分析效率,即获得更多碎片离子峰和更多有关母体离子结构的信息.     

质谱光电离/解离技术和生物分子结构鉴定

质谱是一种广泛应用于化学、生物医学、药学、环境、农业和能源等各领域的分子结构鉴定技术,这种技术通过准确测定分子离子和碎片离子的质量-电荷比来推导分子结构。如何将试样中待测组分有效气化、离子化,转变为具有不同质-荷比的气态离子是质谱仪器和分析方法研究的关键。基于不同物理化学原理的电离、解离方法各有特点,适合不同分析目的。常见的软电离技术一般产生稳定的偶电子离子,往往需要与其他技术联用才能实现分子离子的进一步解离。除了基于碰撞活化和电子得失的两类常见解离方法,光解离技术利用波长/能量可调控的光辐射来使样品分子电离,并引发特定化学键断裂。本文旨在综述不同电离/解离技术,重点探讨近年来发展的红外和紫外光电离/解离技术基本工作原理、仪器特点及其在生物分子(包括有机小分子、蛋白质、核酸和多糖等)结构鉴定中的应用。     

振动态选择的NO2+离子e3B2态解离生成氧离子通道的动力学

结合最新的阈值光电子-光离子符合速度成像技术和同步辐射光电离, 开展了振动态选择的NO₂⁺离子e³B₂态解离动力学研究. 在18.8-19.2 eV范围内获得的NO₂⁺离子e³B₂态的振动分辨阈值光电子谱与前人结果基本符合, 而由e³B₂态(0,0,0)和(1,0,0)振动能级解离生成的O⁺碎片离子的符合速度成像清楚地显示出多个圆环结构, 表明解离过程中生成了多种具有不同速度的O⁺离子, 对应中性解离碎片NO分子处于不同的内态. 通过速度和角度积分, 我们分别获得了解离过程中释放的总平动能分布和O⁺离子的角度分布, 其中两振动态选择的NO₂⁺离子解离生成的NO分子X²Π态振动分布十分相似, 主要布居的振动量子数为3-5. 解离释放的可资用能近似平均分配到碎片的平动能和内能, 其中碎片总平动能约占52%, 内能约占48%. 此外, O⁺离子的各向异性参数β约为0.3, 且不随NO(X²Π)振动量子数而剧烈变化.     

Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS3 of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.     

Systematic Comparison of Ultraviolet Photodissociation and Electron Transfer Dissociation for Peptide Anion Characterization

Ultraviolet photodissociation at 193?nm (UVPD) and negative electron transfer dissociation (NETD) were compared to establish their utility for characterizing acidic proteomes with respect to sequence coverage distributions (a measure of product ion signals across the peptide backbone), sequence coverage percentages, backbone cleavage preferences, and fragmentation differences relative to precursor charge state. UVPD yielded significantly more diagnostic information compared with NETD for lower charge states (n????2), but both methods were comparable for higher charged species. While UVPD often generated a more heterogeneous array of sequence-specific products (b-, y-, c-, z-, Y-, d-, and w-type ions in addition to a- and x- type ions), NETD usually created simpler sets of a/x-type ions. LC-MS/UVPD and LC-MS/NETD analysis of protein digests utilizing high pH mobile phases coupled with automated database searching via modified versions of the MassMatrix algorithm was undertaken. UVPD generally outperformed NETD in stand-alone searches due to its ability to efficiently sequence both lower and higher charge states with rapid activation times. However, when combined with traditional positive mode CID, both methods yielded complementary information with significantly increased sequence coverage percentages and unique peptide identifications over that of just CID alone.     

Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

Ultraviolet photodissociation of chromophore-labeled oligosaccharides via reductive amination and hydrazide conjugation

The fragmentation patterns of hydrazide-conjugated and reductively aminated oligosaccharides, including lacto-N-fucopentaoses and lacto-N-difucohexaoses, produced on collisionally induced dissociation (CID) and ultraviolet photodissociation (UVPD) in a quadrupole ion trap are presented. The two derivatization methods generate different cross-ring cleavages on UVPD and CID. UVPD of hydrazide-conjugated oligosaccharides yield predominant (2, 4)A-type cross-ring cleavage ions. In contrast, UVPD of aminated oligosaccharides results mainly in (0, 1)A-type ions. Moreover, more extensive dual-cleavage pathways (i.e. internal fragment ions) were observed on UVPD.     

Ion trap collision-induced dissociation of locked nucleic acids

Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3′C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics.     

Dipolar DC induced collisional activation of non‐dissociated electron‐transfer products

The application of electron transfer and dipolar direct current induced collisional activation (ET‐DDC) for enhanced sequence coverage of peptide/protein cations is described. A DDC potential is applied across one pair of opposing rods in the high‐pressure collision cell of a hybrid quadrupole/time‐of‐flight tandem mass spectrometer (QqTOF) to induce collisional activation, in conjunction with electron transfer reactions. As a broadband technique, DDC can be employed for the simultaneous collisional activation of all the first‐generation charge‐reduced precursor ions (eg, electron transfer no‐dissociation or ETnoD products) from electron transfer reactions over a relatively broad mass‐to‐charge range. A systematic study of ET‐DDC induced collision activation on peptide/protein cations revealed an increase in the variety (and abundances) of sequence informative fragment ions, mainly c‐ and z‐type fragment ions, relative to products derived directly via electron transfer dissociation (ETD). Compared with ETD, which has low dissociation efficiency for low‐charge‐state precursor ions, ET‐DDC also showed marked improvement, providing a sequence coverage of 80% to 85% for all the charge states of ubiquitin. Overall, this method provides a simple means for the broadband collisional activation of ETnoD ions in the same collision cell in which they are generated for improved structural characterization of polypeptide and protein cations subjected to ETD.     

Peptide and protein quantification using iTRAQ with electron transfer dissociation

Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides produces c- and z -type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage of the N-C(alpha) bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (average error < 10%). Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively.     

Specific UV photodissociation of tyrosyl-containing peptides in multistage mass spectrometry

UV photodissociation (UVPD) at 262 nm has been carried out on protonated tyrosyl-containing peptides formed by trypsin digestion of apo-transferrin. Under UVPD, the main event is the fragmentation of the C(alpha)-C(beta) bond of the tyrosyl residues leading to a radical ion 107 Da below the precursor ion. The dissociation rate of this specific cleavage appears to be strongly dependent on the peptide sequence and is more prominent on the singly protonated species than on the doubly protonated state. The fragmentation spectra resulting from collisional activation of the protonated even-electron native peptides and of the odd-electron radical species prepared by UVPD are dominated by y-type backbone cleavages. A comparison of their respective y-ion pattern shows complementarities since the combination of both increases the sequence coverage of the peptide sequence. The specific detection of the neutral loss of 107 Da from peptides witnesses the content of at least one tyrosyl residue and, though preliminary, is proposed as a potential new filtering strategy during protein database searching.     

'Top-down' characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trap

The gas-phase fragmentation reactions of a series of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase have been examined by multistage tandem mass spectrometry (MS/MS and MS(3)) in a linear quadrupole ion trap in order to explore the utility of this instrumentation for routine 'top-down' recombinant protein characterization. Following a rapid low resolution survey of the fragmentation behavior of the precursor ions from the wild type (WT) protein, selected charge states were subjected to detailed structural characterization by using high resolution 'zoom' and 'ultrazoom' resonance ejection MS/MS product ion scans. Dissociation of the [M + 18H](18+) charge state yielded a range of product ions from which extensive sequence information could be derived. In contrast, dissociation of the [M + 20H](20+) charge state resulted in a single dominant y(96) product ion formed by fragmentation between adjacent Ile/Gly residues, with only limited sequence coverage. Further extensive sequence information was readily obtained however, by MS(3) dissociation of this initial product. From the combined MS/MS and MS(3) spectra an overall sequence coverage of 66.9%, with fragmentation of 85 of the 127 amide bonds within the WT protein, was obtained. MS/MS and MS(3) of three of the four site-directed mutagenesis products (E29A), (Y61F) and (E81A) were found to yield essentially identical product ion spectra to the WT protein, indicating that these modifications had no significant influence on the fragmentation behavior. The specific site of modification could be unambiguously determined in each case by characterization of product ions resulting from fragmentation of amide bonds on either side of the mutation site. In contrast, MS/MS and MS(3) of the K107A mutant led to significantly different product ion spectra dominated by cleavages occurring N-terminal to proline, which restricted the ability to localize the modification site to within only an 8 amino acid region of the sequence. This work highlights the need for further studies to characterize the charge state, sequence and structural dependence to the low energy collision induced dissociation reactions of multiply protonated intact protein ions.     

Collisionally activated dissociation and electron capture dissociation provide complementary structural information for branched permethylated oligosaccharides

Doubly charged sodiated and permethylated linear malto-oligosaccharides ({Glc}6-{Glc}9), branched N-linked glycans (high-mannose type GlcNAc2Man5-9, and complex asialo- and disialylated-biantennary glycans) were analyzed by tandem mass spectrometry using collisionally-activated dissociation (CAD) and "hot" electron capture dissociation (ECD) available in a custom-built ESI FTICR mass spectrometer. For linear permethylated malto-oligosaccharides, both CAD and "hot" ECD produced glycosidic cleavages (B, Y, C, and Z ions), cross-ring cleavages (A- and X-type), and internal cleavages (B/Y and C/Y type) to provide sequence and linkage information. For the branched N-linked glycans, CAD and "hot" ECD provided complementary structural information. CAD generated abundant B and Y fragment ions by glycosidic cleavages, whereas "hot" ECD produced dominant C and Z ions. A-type cross-ring cleavages were present in CAD spectra. Complementary A- and X-type cross-ring fragmentation pairs were generated by "hot" ECD, and these delineated the branching patterns and linkage positions. For example, 0, 4An and 3, 5An ions defined the linkage position of the major branch as the 6-position of the central core mannose residue. The internal fragments observed in CAD were more numerous and abundant than in "hot" ECD spectra. Since the triply charged (sodiated) molecular ion of the permethylated disialylated-biantennary N-linked glycan has relatively high abundance, it was isolated and fragmented in a "hot" ECD experiment and extensive fragment ions (glycosidic and complementary pairs of cross-ring cleavages) were generated to fully confirm the sequence, branching, and linkage assignments for this glycan.