Sequencing Lys-N Proteolytic Peptides by ESI and MALDI Tandem Mass Spectrometry

In this study, we explored the MS/MS behavior of various synthetic peptides that possess a lysine residue at the N-terminal position. These peptides were designed to mimic peptides produced upon proteolysis by the Lys-N enzyme, a metalloendopeptidase issued from a Japanese fungus Grifola frondosa that was recently investigated in proteomic studies as an alternative to trypsin digestion, as a specific cleavage at the amide X-Lys chain is obtained that provides N-terminal lysine peptide fragments. In contrast to tryptic peptides exhibiting a lysine or arginine residue solely at the C-terminal position, and are thus devoid of such basic amino acids within the sequence, these Lys-N proteolytic peptides can contain the highly basic arginine residue anywhere within the peptide chain. The fragmentation patterns of such sequences with the ESI-QqTOF and MALDI-TOF/TOF mass spectrometers commonly used in proteomic bottom-up experiments were investigated.     

Differentiation of Regioisomeric Esters of Sucrose by Ionspray Tandem Mass Spectrometry

Abstract

Structural characterization and differentiation of distinct regioisomenc esters of sucrose were obtained using lonspray ionization and low energy tandem mass spectrometry. Low energy CAD MS/MS analyses of the protonated molecules [M + H]⁺ provided characteristic fingerprint patterns, and permitted differentiation of the various regioisomers. MS/MS analyses of selected intermediate fragment ions formed during the ionization process provided additional structural data, and established the fragmentation routes of their [M + H]⁺ precursors.     

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b_n-1 + H₂O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H₂O and NH₃) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y_m-1 ion, i.e., to the loss of the N-terminal residue following the a₁-y_m–1 fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N- and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.     

Capillary-Channeled Polymer (C-CP) Films as Processing Platforms for Protein Analysis by Matrix-Assisted Laser/Desorption Ionization Mass Spectrometry (MALDI-MS)

Polypropylene (PP) capillary-channeled polymer (C-CP) films have parallel, μm-sized channels that induce solution wicking via capillary action. Efficient mass transport from the solution phase to the channel surface leads to adsorption of hydrophobic protein solutes. The basic premise by which C-CP films can be used as media to manipulate analyte solutions (e.g., proteins in buffer), for the purpose of desalting or chromatographic separation prior to MALDI-MS analysis is presented here. Cytochrome c and myoglobin prepared in a Tris-HCl buffer, and ribonuclease A, lysozyme, and transferrin prepared in phosphate buffered saline (PBS), are used as the test solutions to demonstrate the desalting concept. Protein analysis is performed after deposition on a C-CP film with and without a water washing step, followed by spray deposition of a typical sinapinic acid matrix. Extracted MALDI mass spectra exhibit much improved signal-to-noise characteristics after water washing. A mixture of cytochrome c and myoglobin (2 μL of 2.5 μM each in Tris-HCl buffer) was applied, washed with water and spatially separated via simple capillary action (wicking) using a reversed-phase solvent composition of 0.1% trifluoroacetic acid (TFA) in 50:50 acetonitrile (ACN):H₂O. Subsequent application of sinapinic acid followed by imaging of the film using MALDI-MS reveals that as the protein solution is wicked down the film, separation occurs.     

Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry

The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationized MALDI matrices, Na⁺(MALDI), with Xe is studied as a function of kinetic energy. The MALDI matrices examined here include: nicotinic acid, quinoline, 3-aminoquinoline, 4-nitroaniline, picolinic acid, and 3-hydroxypicolinic acid. In all cases, the primary dissociation pathway corresponds to endothermic loss of the intact MALDI matrix. The cross section thresholds are interpreted to yield zero and 298 K Na⁺−MALDI bond dissociation energies (BDEs), or sodium cation affinities, after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* and MP2(full)/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory are used to characterized the structures and energetics for these systems. The calculated BDEs exhibit very good agreement with the measured values for most systems. The experimental and theoretical Na⁺−MALDI BDEs determined here are compared with those previously measured by cation transfer equilibrium methods.     

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N′H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.      

基质辅助激光解吸电离质谱分析糖类物质

基质辅助激光解吸电离质谱（MALDI-MS）是一种样品无需衍生、图谱解析简单、灵敏度高、快速便捷的分析生物样品结构的方法,已被广泛用于糖类物质的结构分析。此技术与HPLC、糖苷酶外切技术以及各种串联质谱等技术结合使用,可给出糖类物质详细的结构信息。本文介绍了基质辅助激光解吸（MALDI）离子化技术的原理、特点、与飞行时间质量分析器（TOF）联用时的相关技术和裂解方式,以及MALDI-MS在分析糖类物质时选用的基质、样品的制备、糖链碎片分析的方法和在不同糖型分析中的应用,展示了它的发展前景。随着MALDI对糖类物质分析时基质的改进、质谱分辨率的提高、质量检测范围的扩大,MALDI-MS技术必将成为糖类物质分析中强有力的工具。     

MALDI Mass Spectrometry Analysis of Human Hemoglobin

IntroductionThemolecularweightofaproteinhasalwaysbeenrecognizedasanimpor-tantanalyticalparameterinbiochemistry.Sodiumdodecylsulfata-polyacry-lamidegelelectrophoresis(SDS-PAGE)isuniversallyusedtopurifyproteins,af-terseparationmo1ecularweightsareroutinelydeterminedbycomparisonofthemigrationrateoftheproteintobedeterminedtothatofasetofstandardpro-teins.However,ahighaccuracy(e.g.,to相似文献   

Differentiation of Regioisomeric Aromatic Ketocarboxylic Acids by Positive Mode Atmospheric Pressure Chemical Ionization Collision-Activated Dissociation Tandem Mass Spectrometry in a Linear Quadrupole Ion Trap Mass Spectrometer

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS ⁿ ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.     

多级质谱法测定Axinastatin 1环肽序列及其断裂机理研究

对具有抗癌活性的海洋环肽Axinastatin 1进行化学合成. 采用多级质谱法对合成环肽进行序列测定. 线性前体测序依据b_x－y_z断裂路径, 在同一张MS²谱中利用b和y离子所提供序列信息的互补来实现. 环肽测序依据b_x→b_x－1断裂路径, 每一级MS由b离子的C端碰撞掉一个氨基酸残基直到MS⁶, 得到2套b离子, 根据它们所提供序列信息的互补可准确测定环肽序列并推断其环结构, 同时观察到b离子重排现象. 讨论了上述断裂与重排的路径和机理, 并利用半经验量子化学PM3和AM1两种算法计算了碎片的生成焓, 验证了路径的合理性. 由离子b_5PN的生成焓偏高和其重排间的联系尝试提出过渡结构假设.     

Sequence Elucidation of an Unknown Cyclic Peptide of High Doping Potential by ETD and CID Tandem Mass Spectrometry

Identification of an unknown substance without any information remains a daunting challenge despite advances in chemistry and mass spectrometry. However, an unknown cyclic peptide in a sample with very limited volume seized at a Pennsylvania racetrack has been successfully identified. The unknown sample was determined by accurate mass measurements to contain a small unknown peptide as the major component. Collision-induced dissociation (CID) of the unknown peptide revealed the presence of Lys (not Gln, by accurate mass), Phe, and Arg residues, and absence of any y-type product ion. The latter, together with the tryptic digestion results of the unusual deamidation and absence of any tryptic cleavage, suggests a cyclic structure for the peptide. Electron-transfer dissociation (ETD) of the unknown peptide indicated the presence of Gln (not Lys, by the unusual deamidation), Phe, and Arg residues and their connectivity. After all the results were pieced together, a cyclic tetrapeptide, cyclo[Arg-Lys-N(C₆H₉)Gln-Phe], is proposed for the unknown peptide. Observations of different amino acid residues from CID and ETD experiments for the peptide were interpreted by a fragmentation pathway proposed, as was preferential CID loss of a Lys residue from the peptide. ETD was used for the first time in sequencing of a cyclic peptide; product ions resulting from ETD of the peptide identified were categorized into two types and named pseudo-b and pseudo-z ions that are important for sequencing of cyclic peptides. The ETD product ions were interpreted by fragmentation pathways proposed. Additionally, multi-stage CID mass spectrometry cannot provide complete sequence information for cyclic peptides containing adjacent Arg and Lys residues. The identified cyclic peptide has not been documented in the literature, its pharmacological effects are unknown, but it might be a “designer” drug with athletic performance-enhancing effects.     

有机异构体的质谱分析简介

本文介绍了用于有机异构体辨析的几种质谱方法，并综述了它们在五类异构体中的应用。     

Tandem Mass Spectrometry of Trimethylsilyl-Terminated Poly(Dimethylsiloxane) Ammonium Adducts Generated by Electrospray Ionization

Ammonium adducts of trimethylsilyl-terminated poly(dimethylsiloxane) (CH₃-PDMS) produced by electrospray ionization were submitted to collision induced dissociation and revealed a particular MS/MS behavior: the same three main product ions at m/z 221, 295, and 369 were always generated in very similar relative abundances regardless of the size of the precursor ion. Combining accurate mass measurements and ab initio calculation allowed very stable cyclic geometries to be obtained for these ionic species. Dissociation mechanisms were proposed to account for the three targeted ions to be readily generated in a two-step or a three-step reaction from any CH₃-PDMS ammonium adducts. A second set of three product ions was also observed with low abundance at m/z 207, 281, and 355, which were shown in MS³ experiments to be formed in secondary reactions. An alternative dissociation process was shown to consist of a concerted elimination of ammonia and methane and the need for a methyl of an end-group to be involved in the released methane molecule would account for this reaction to mainly proceed from the smallest precursor ions.     

Comparision of FAB and MALDI Mass Spectrometry of Ginsenosides

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Recent Advances in MALDI Mass Spectrometry of Polymers

Matrix-Assisted Laser Desorption/Ionization (MALDI) allows the identification of repeat units and end groups, the structural analysis of linear and cyclic oligomers, and the estimate of composition and sequence for copolymers. MALDI has also been applied to the measurement of molar mass distributions in polymers and to the study of thermal and oxidative processes in polymers. This paper illustrates the detection of self-association in macromolecules made by coupling MALDI and Size Exclusion Chromatography (SEC), the investigation of polymer oxidation phenomena, and the characterization of copolymers formed in the processing of reactive polymer blends.     

刺五加中苷类化合物的电喷雾多级串联质谱

采用小柱层挤、电喷雾多级串联质谱方法，通过分子量及正负离子多级串联质谱的信息对刺五加提取物中的有效成分刺五加苷B、刺五加苷E进行了定性分析，并提出了其电喷雾质谱碎裂机理。该方法样品处理简单，分析速度快且灵敏度高，实验重复性好，适宜于作为刺五加有效成分鉴定的指纹图谱，对刺五加药品质量控制具有重要意义。     

利用(+)ESI-MS-MS方法分析研究脱氧四核苷酸的裂解特征

细胞中存在很多金属离子参与DNA及其组成部分的重要的生物过程.质谱作为1种重要的分析方法,能用以考察这些金属离子和DNA在分子水平的相互作用,确定金属离子和生物分子的结合位点,并检测金属离子对于生物分子的性质和反应性的影响.本研究利用(+)ESI-MS-MS考察了3个四碱基DNA分子d(TGAC)、d(GTAC)、d(ATAT)的[M+Na]+、[M+K]+的质谱行为,这些金属离子与同1分子的[M+H]+的裂解具有明显的差异;推测为不同的离子在DNA上的加合位置不同,导致质谱行为的差异.     

MALDI Mass Spectrometry Imaging of Neuronal Cell Cultures

Mass spectrometry imaging (MSI) provides the ability to detect and identify a broad range of analytes and their spatial distributions from a variety of sample types, including tissue sections. Here we describe an approach for probing neuropeptides from sparse cell cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MSI—at single cell spatial resolution—in both MS and tandem MS modes. Cultures of Aplysia californica neurons are grown on an array of glass beads embedded in a stretchable layer of Parafilm M. As the membrane is stretched, the beads/neurons are separated physically and the separated beads/neurons analyzed via MALDI TOF MS. Compared with direct MS imaging of samples, the stretching procedure enhances analyte extraction and incorporation into the MALDI matrix, with negligible analyte spread between separated beads. MALDI tandem MSI using the stretched imaging approach yields localization maps of both parent and fragment ions from Aplysia pedal peptide, thereby confirming peptide identification. This methodology represents a flexible platform for MSI investigation of a variety of cell cultures, including functioning neuronal networks.     

The Detection and Stability of DNA Duplexes Probed by MALDI Mass Spectrometry

Matrix‐assisted laser desorption/ionization (MALDI) with nonacidic matrices is shown to generate intact gas‐phase ions of double‐stranded DNA. Control experiments show that specific DNA duplexes are detected by this method, while nonspecific adducts form only when high monomer concentrations are present in the MALDI sample. The relative intensity of the duplex‐ion signal is found to reflect the solution‐phase stability of the double‐stranded DNA.     

MALDI In-Source Decay Mass Spectrometry of Polyamidoamine Dendrimers

We report using MALDI-ISD (in-source decay) mass spectrometry (MS) to characterize highly branched synthetic polymers of polyamidoamine (PAMAM) dendrimer. This inherently monodisperse polymer possesses dendritic branches networked by tertiary amines and an amide functionality in each repeating unit. Among various ISD matrices examined, 2,5-DHB was the most efficient, yielding 33 fragments produced by single- or multiple-bond cleavages. Detailed analysis revealed that cleavages at tertiary amine sites (S- and E-type fragments) were the most pronounced, with various other cleavages around amide groups. The fragmentation mechanism appeared to follow the radical-induced dissociation pathway. In addition, the matrix dependence of PAMAM MALDI-ISD differed from that of peptides/proteins. The observed fragments provided rich structural information, which was suitable to characterize dendritic polymers.