Mass Spectrometry: Current Research Articles
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On this page considered biochemistry journals:
Mass Spectrometry Reviews - published by
Wiley Interscience -
Journal of Mass Spectrometry - published by
Wiley Interscience -
Current research articles of the mentioned
journals:
Femtosecond laser ablation inductively coupled plasma mass spectrometry: Fundamentals and capabilities for depth profiling analysis
Laser ablation coupled to inductively coupled plasma mass spectrometry has become a versatile and powerful analytical method for direct solid analysis. The applicability has been demonstrated on a wide variety of samples, where major, minor, and trace element concentrations or isotope ratio determinations have been of interest. The pros and cons of UV-nsec laser ablation have been studied in detail, and indicate that aerosol generation, aerosol transport, and aerosol excitation-ionization within the ICP contribute to fractionation effects, which prevent this method from a more universal application to all matrices and all elements. Recent progresses in IR-fs and UV-fs laser ablation coupled to ICP-MS have been reported, which increase the inter-matrix and multi-element quantification capabilities of this method. These fundamental improvements in LA-ICP-MS are of significant importance for entering new applications in material science and related research fields. In particular, because coatings (conducting and non-conducting) consist of single or multilayers of various elemental composition and of different thickness (nm-mm range), significant progress in the field of depth profiling with fs-laser ablation can be expected. Therefore, in-depth profile analysis of polymers, semiconductors, and metal sample investigations, using ultra-fast laser ablation for sampling and the currently achievable figures of merit, are discussed. In this review manuscript, the enhanced capabilities of fs-LA-ICP-MS for direct solid sampling are highlighted, and it is discussed about current methods used for quantitative analysis and depth profiling, the ablation process of UV-ns and UV-fs, the influence of the laser beam profile, aerosol structure and transport efficiency, as well as the influence of the ICP-MS (e.g., vaporization and ionization efficiency in the plasma, and type of mass analyzer). © 2008 Wiley Periodicals, Inc. Mass Spectrom. Rev.
Mass spectrometry in systems biology: An overview
As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Mass and lifetime measurements of exotic nuclei in storage rings
Mass and lifetime measurements lead to the discovery and understanding of basic properties of matter. The isotopic nature of the chemical elements, nuclear binding, and the location and strength of nuclear shells are the most outstanding examples leading to the development of the first nuclear models. More recent are the discoveries of new structures of nuclides far from the valley of stability. A new generation of direct mass measurements which allows the exploration of extended areas of the nuclear mass surface with high accuracy has been opened up with the combination of the Experimental Storage Ring ESR and the FRragment Separator FRS at GSI Darmstadt. In-flight separated nuclei are stored in the ring. Their masses are directly determined from the revolution frequency. Dependent on the half-life two complementary methods are applied. Schottky Mass Spectrometry SMS relies on the measurement of the revolution frequency of electron cooled stored ions. The cooling time determines the lower half-life limit to the order of seconds. For Isochronous Mass Spectrometry IMS the ring is operated in an isochronous ion-optical mode. The revolution frequency of the individual ions coasting in the ring is measured using a time-of-flight method. Nuclides with lifetimes down to microseconds become accessible. With SMS masses of several hundreds nuclides have been measured simultaneously with an accuracy in the 2 × 10-7-range. This high accuracy and the ability to study large areas of the mass surface are ideal tools to discover new nuclear structure properties and to guide improvements for theoretical mass models. In addition, nuclear half-lives of stored bare and highly charged ions have been measured. This new experimental development is a significant progress since nuclear decay characteristics are mostly known for neutral atoms. For bare and highly charged ions new nuclear decay modes become possible, such as bound-state beta decay. Dramatic changes in the nuclear lifetime have been observed in highly charged ions compared to neutral atoms due to blocking of nuclear decay channels caused by the modified atomic interaction. High ionization degrees prevail in hot stellar matter and thus these experiments have great relevance for the understanding of the synthesis of elements in the universe and astrophysical scenarios in general. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Sieve-based device for MALDI sample preparation. I. Influence of sample deposition conditions in oligonucleotide analysis to achieve significant increases in both sensitivity and resolution
Spraying of oligonucleotide-matrix solutions through a stainless steel (ss) sieve (38 µm, 450 mesh) leads to the formation, on the matrix-assisted laser desorption/ionization (MALDI) sample holder, of uniformly distributed microcrystals, well separated from each other. When the resulting sample holder surface is irradiated by laser, abundant molecular species form, with a clear increase in both intensity and resolution with respect to values obtained by 'Dried Droplet', 'Double Layer', and 'Sandwich' deposition methods. In addition, unlike the usual situation, the sample is perfectly homogeneous, and identical spectra are obtained by irradiating different areas. On one hand, the data indicate that this method is highly effective for oligonucleotide MALDI analysis, and on the other, that it can be validly employed for fully automated MALDI procedures. Copyright © 2008 John Wiley & Sons, Ltd.
Photoionization studies on various quinones by an infrared laser desorption/tunable VUV photoionization TOF mass spectrometry
Photoionization and dissociative photoionization characters of six quinones, including 1,2-naphthoquinone (1,2-NQ), 1,4-naphthoquinone (1,4-NQ), 9,10-phenanthroquinone (PQ), 9,10-anthraquinone (AQ), benz[a]- anthracene-7,12-dione (BAD) and 1,2-acenaphthylenedione (AND) have been studied with an infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IR LD/VUV PIMS) technique. Mass spectra of these compounds are obtained at different VUV photon energies. Consecutive losses of two carbon monoxide (CO) groups are found to be the main fragmentation pathways for all the quinones. Detailed dissociation processes are discussed with the help of ab initio B3LYP calculations. Ionization energies (IEs) of these quinones and appearance energies (AEs) of major fragments are obtained by measuring the photoionization efficiency (PIE) spectra. The experimental results are in good agreement with the theoretical data. Copyright © 2008 John Wiley & Sons, Ltd.
Plant proteomics: Concepts, applications, and novel strategies for data interpretation
Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics. © 2008 Wiley Periodicals, Inc. Mass Spectrom. Rev.
Mass spectrometry-based proteomics in reproductive medicine
The emergence of powerful mass spectrometry-based proteomic techniques has added a new dimension to the field of biomedical research. Application of these high throughput methodologies in pregnancy-related pathology has contributed to the comprehension of the underlying pathophysiologies and the successful identification of relevant protein biomarkers that can potentially change early diagnosis and treatment of several medical conditions related to human pregnancy. Most of the existing research on human reproduction and gestation has focused on follicular fluid, cervical/vaginal fluid, and amniotic fluid. Although proteome technologies in reproductive medicine research are not as yet widely applied, characterization of the proteome of reproductive fluids can be expected to significantly improve maternal healthcare. This article aims to summarize the applications of mass spectrometry based technology on the most important and specific biological fluids related to reproduction and gestation. © 2008 Wiley Periodicals, Inc. Mass Spectrom. Rev.
When electrons meet molecular ions and what happens next: Dissociative recombination from interstellar molecular clouds to internal combustion engines
The interaction of matter with its environment is the driving force behind the evolution of 99% of the observed matter in the universe. The majority of the visible universe exists in a state of weak ionization, the so called fourth state of matter: plasma. Plasmas are ubiquitous, from those occurring naturally; interstellar molecular clouds, cometary comae, circumstellar shells, to those which are anthropic in origin; flames, combustion engines and fusion reactors. The evolution of these plasmas is driven by the interaction of the plasma constituents, the ions, and the electrons. One of the most important subsets of these reactions is electron-molecular ion recombination. This process is significant for two very important reasons. It is an ionization reducing reaction, removing two ionised species and producing neutral products. Furthermore, these products may themselves be reactive radical species which can then further drive the evolution of the plasma. The rate at which the electron reacts with the ion depends on many parameters, for examples the collision energy, the internal energy of the ion, and the structure of the ion itself. Measuring these properties together with the manner in which the system breaks up is therefore critical if the evolution of the environment is to be understood at all. Several techniques have been developed to study just such reactions to obtain the necessary information on the parameters. In this paper the focus will be on one the most recently developed of these, the Ion Storage Ring, together with the detection tools and techniques used to extract the necessary information from the reaction. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Live single-cell video-mass spectrometry for cellular and subcellular molecular detection and cell classification
The molecular content from the cytoplasm of a live, single mammalian cell and its organelle were trapped with a nano-electrospray ionization (ESI) tip acting as a micropipette under a video microscope, and hundreds of small molecular peaks were detected by direct nano-ESI mass spectrometry (MS). Granule- or cytoplasm-specific peaks in a mast cell (RBL 2H3) model were extracted by paired t-test to demonstrate their specific localization. Some of the typical and specific molecules were successfully identified by MS/MS analysis. This method was also applied to the cell classification of seven types of cell lines at the single-cellular level by principal component analysis (PCA), revealing seven clusters in the multivariate score plot. Copyright © 2008 John Wiley & Sons, Ltd.
Theoretical and experimental study of tropylium formation from substituted benzylpyridinium species
Fragmentation pathways of unsubstituted and substituted benzylpyridinium compounds were investigated using mass-analysed kinetic energy (MIKE) technique in combination with high level of quantum chemical calculations in the gas phase. Fast atom bombardment (FAB) source was used for ionisation of the studied compounds. The formation of both benzylium and tropylium species were investigated. Hybrid Hartree-Fock/Density Functional Theory calculations have been performed to assess the geometries and the energies of the transition states and intermediates. For each cases, different reaction pathways were investigated, and particularly in the case of the formation of tropylium species, the formation of the seven-membered ring before or after the loss of pyridine were studied. The effect of para-methyl and para-methoxy substituents on the activation energy of the rearrangement process to form thermodynamically stable tropylium compounds has been studied. Theoretical calculations showed competition between direct bond cleavage and rearrangement reactions to form benzylium and tropylium compounds, respectively. Experimental results also suggested that the rearrangement process takes place to yield stable tropylium under "soft ionisation techniques", such as FAB. Copyright © 2008 John Wiley & Sons, Ltd.
Sensitivity of redox reactions of dyes to variations of conditions created in mass spectrometric experiments
Redox behaviour of four imidazophenazine dye derivatives under mass spectrometric conditions of matrix-assisted laser desorption/ionization (MALDI), laser desorption/ionization (LDI) from metal and graphite surface, electrospray, low temperature secondary ion mass spectrometry (LT SIMS) and fast atom bombardment (FAB) was studied and distinctions in the reduction-dependent spectral patterns were analyzed from the point of view of different quantities of protons and electrons available for reduction in different techniques. The reduction products [M + 2H]+[bull], [M + 3H]+ and M-[bull], [M + H]- were observed in the positive and negative ion modes, respectively, which permitted to suggest independent occurrence of reduction and protonation/deprotonation processes. LDI from graphite substrate was the only technique that allowed us to obtain abundant negative ions of all dye derivatives. The yield of field ionization (FI) or field desorption (FD) mechanism to ion formation under LDI from rough graphite surface has been addressed. The sensitivity of reduction of the dyes to variation of reduction-initiating agents confirms high redox activity of the dyes essential for their functioning in natural and artificial systems. Copyright © 2008 John Wiley & Sons, Ltd.
Targeted identification of phosphorylated peptides by off-line HPLC-MALDI-MS/MS using LC retention time prediction
Protein phosphorylation is a type of posttranslational modification which plays an important role in cell regulation and signal transduction. Because of its biological relevance, a considerable amount of interest has been paid to the development of efficient techniques for phosphopeptide analysis. Although advances in MS control have enabled the high-throughput discovery of proteins from limited amounts of sample, automated selection of MS/MS precursor ions based on intensity alone can significantly hamper the detection of low-abundance phosphopeptides. On the basis of the observation that the introduction of a phosphate moiety does not dramatically change peptide retention time in reverse-phase chromatography, phosphopeptide specific MS/MS fragmentation attempts based on LC retention time and m/z were evaluated using a standard protein mixture, then using in vitro phosphorylated myelin basic protein. Results indicated that the majority (98%) of phosphopeptides identified eluted within a ± 4-min window of the predicted LC elution time. While studies presented here are primarily proof of concept in nature, data suggest that the use of LC retention time prediction could be a valuable constraint for the identification of phosphopeptides within a set of off-line LC deposited sample spots. It is expected that the development of these methods will not only permit the targeted identification of protein phosphorylation sites but also allow the in-depth analysis of the dynamic events linked to the posttranslational modification. Copyright © 2008 John Wiley & Sons, Ltd.
The McLafferty rearrangement in the Glu residue in a cyclic lipopeptide determined by Q-TOF MS/MS
The intraresidue rearrangement and loss of the side chain of the Glu residue was found through MS/MS analysis of both original and methanol-esterified lipopeptides. Both Glu and Asp residues in the cyclic lipopeptide were esterified. The MS/MS results showed that the loss of fragment 72 or 86 was induced by McLafferty-type rearrangement from the Glu or esterified Glu. The mechanism of loss of the Glu residue can be used to determine or to corroborate the existence of the Glu and to help understand the fragment formation in MS/MS. The cleavage mechanism and m/z intensities imply that the sodium ion was easier attached and the cleavage would easily occur at specific sites. Copyright © 2008 John Wiley & Sons, Ltd.
Differences between collisionally activated and electron-transfer dissociations found for CH2X2(X = Cl, Br, and I) by using alkali-metal targets
High-energy collisionally activated dissociation (HE-CAD) and high-energy electron- transfer dissociation (HE-ETD) on collisions with alkali-metal targets (Cs, K, and Na) were investigated for CH2X2+ (X = Cl, Br, and I) ions by tandem mass spectrometry (MS/MS). In the HE-CAD spectra observed, peaks associated with CH2X+ ions formed by a loss of a halogen atom are always predominant regardless of precursor ions and target metals. The observation of the predominant CH2X+ ions is explained by the lowest energy levels of the fragments of CH2X+ + X among the possible fragment energy levels and internal-energy distribution in HE-CAD. In the charge-inversion spectra, relative peak intensities of the negative ions formed by HE-ETD strongly depend on the precursor ions and the target metals. While the CHCl2- ion was predominant in the spectra of CH2Cl2+ regardless of target species, the most intense peaks in those of CH2Br2+ and CH2I2+ were ascribed to either Br- or CH2Br- and either I- or I2-, respectively, depending on the target metals. The dependence of the relative intensities of the fragment ions by HE-ETD on the precursor ions and target species are discussed on the basis of the energy levels of the neutral fragments and the narrow internal-energy distribution resulting from the near-resonant neutralization. It was demonstrated that HE-ETD using the alkali-metal targets provided rich information on the dissociation of the neutral species. Copyright © 2008 John Wiley & Sons, Ltd.
IRMPD spectra of Gly·NH4+ and proton-bound betaine dimer: evidence for the smallest gas phase zwitterionic structures
Zwitterionic structures exist extensively in biological systems and the electric field resulting from zwitterion formation is the driving force for determination of the properties, function and activity of biological molecules, such as amino acids, peptides and proteins. It is of considerable interest and import to investigate the stabilization of zwitterionic structures in the gas phase. Infrared multiple photon dissociation (IRMPD) spectroscopy is a very powerful and sensitive technique, which may elucidate clearly the structures of both ions and ionic clusters in the gas phase, since it provides IR vibrational fingerprint information. The structures of the clusters of glycine and ammonium ion and of the betaine proton-bound homodimer have been investigated using IRMPD spectroscopy, in combination with electronic structure calculations. The experimental and calculated results indicate that zwitterionic structure of glycine may be effectively stabilized by an ammonium ion. This is the smallest zwitterionic structure of an amino acid to be demonstrated in the gas phase. On the basis of the experimental IRMPD and calculated results, it is very clear that a zwitterionic structure exists in the proton-bound betaine dimer. The proton is bound to one of the carboxylate oxygens of betaine, rather than being equally shared. Investigations of zwitterionic structures in the isolated state are essential for an understanding of the intrinsic characteristics of zwitterions and salt bridge interactions in biological systems. Copyright © 2008 John Wiley & Sons, Ltd.
Calibration laws based on multiple linear regression applied to matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry
Operation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m/z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT-ICR-MS to consistently obtain the same ion population is not readily amenable to matrix-assisted laser desorption/ionization (MALDI) FT-ICR-MS, due to the heterogeneous nature and poor spot-to-spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI-FT-ICR-MS is performed to achieve higher mass measurement accuracy (MMA). Copyright © 2008 John Wiley & Sons, Ltd.
Recognizing [alpha]-, [beta]- or [gamma]-substitution in pyridines by mass spectrometry
A general mass spectrometric method able to recognize the site of substitution of monosubstituted pyridines is described. The method requires that the molecule under investigation forms, upon ionization and dissociation, the respective [alpha]-, [beta]- or [gamma]- pyridinium ion of m/z 78. Pyridinium ions are stable and common fragments of ionized and protonated pyridines and are found to function as appropriate structurally diagnostic fragment ions. They can be identified by their characteristic and nearly identical collision-induced dissociation behavior and distinguished by the combined use of two structurally diagnostic ion/molecule reactions with acetonitrile and 2-methyl-1,3-dioxolane. [alpha]-, [beta]- or [gamma]-substitution in pyridines can, therefore, be securely recognized via an MS-only method based on structurally diagnostic ions and by the inspection of a single molecule (no need for intracomparisons within the whole set of isomers). Copyright © 2008 John Wiley & Sons, Ltd.
Halohydrination of epoxy resins using sodium halides as cationizing agents in MALDI-MS and DIOS-MS
Halohydrination of epoxy resins using sodium halides as cationizing agents in matrix-assisted laser desorption/ionization (MALDI) and desorption ionization on porous silicon mass spectrometry (DIOS-MS) were investigated. Different mass spectra were observed when NaClO4 and NaI were used as the cationizing agents at the highest concentration of 10.0 mM, which is much higher than that normally used in MALDI-MS. MALDI mass spectra of epoxy resins using NaI revealed iodohydrination to occur as epoxy functions of the polymers. The halohydrination also occurred using NaBr, but not NaCl, due to the differences in their nucleophilicities. On the basis of the results of experiments using deuterated CD3OD as the solvent, the hydrogen atom source was probably ambient water or residual solvent, rather than being derived from matrices. Halohydrination also occurred with DIOS-MS in which no organic matrix was used; in addition, reduction of epoxy functions was observed with DIOS. NaI is a useful cationizing agent for changing the chemical form of epoxy resins due to iodohydrination and, thus, for identifying the presence of epoxy functions. Copyright © 2008 John Wiley & Sons, Ltd.
HPTLC/DESI-MS imaging of tryptic protein digests separated in two dimensions
Desorption electrospray ionization mass spectrometry (DESI-MS) was demonstrated as a method to detect and identify peptides from two-dimensional separations of cytochrome c and myoglobin tryptic digests on ProteoChrom HPTLC Cellulose sheets. Data-dependent tandem mass spectra were acquired during lane scans across the TLC plates. Peptides and the corresponding proteins were identified using a protein database search software. Two-dimensional distributions of identified peptides were mapped for each separated protein digest. Sequence coverages for cytochrome c and myoglobin were 81 and 74%, respectively. These compared well with those determined using the more standard HPLC/ESI-MS/MS approach (89 and 84%, respectively). Preliminary results show that use of more sensitive instrumentation has the potential for improved detection of peptides with low Rf values and improvement in sequence coverage. However, less multiple charging and more sodiation were seen in HPTLC/DESI-MS spectra relative to HPLC/ESI-MS spectra, which can affect peptide identification by MS/MS. Methods to increase multiple charging and reduce the extent of sodiation are currently under investigation. Published in 2008 by John Wiley & Sons, Ltd.
Analysis of environmental stress response on the proteome level
Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Issues and opportunities in accelerator mass spectrometry for stable isotopes
Accelerator mass spectrometry (AMS) has developed in the last 30 years many notable applications to the spectrometry of radioisotopes, particularly in radiocarbon dating. The instrumentation science of trace element AMS (TEAMS) that analyzes stable isotopes, also called Accelerator SIMS or MegaSIMS, while unique in many features, has also shared in many of these significant advances and has pushed TEAMS sensitivity to concentration levels surpassing many competing mass spectroscopic technologies. This review examines recent instrumentation developments, the capabilities of the new instrumentation and discernable trends for future development. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Cluster emission and chemical reactions in oxygen and nitrogen ices induced by fast heavy-ion impact
Two ices, O2 and a mixture of O2 and N2, are bombarded by 252Cf fission fragments (FF) ([sim]65 MeV at target surface); the emitted positive and negative secondary ions are analyzed by time-of-flight mass spectrometry (TOF-SIMS). These studies shall enlighten sputtering from planetary and interstellar ices. Three temperature regions in the 28-42-K range are analyzed: (1) before N2 sublimation, in which hybrid chemical species are formed, (2) before O2 sublimation, in which the TOF mass spectrum is dominated by low-mass (O2)p cluster ions and (3) after O2 sublimation, in which (N2)p or (O2)p cluster ions are practically inexistent. In the first region, four hybrid ion series are observed: NOn-1+, N2On-2±, and N4On-4-. In the second region, two positive and negative ion series are identified: (O2)pO± and (O2)pO2±. Their yield distributions are fitted by the sum of two decreasing exponentials, whose decay constants are the same for all series. It is observed that the cluster ion desorption from solid oxygen is very similar to that of other frozen gases, but its yield distribution oscillates with a three- or six-atom periodicity, suggesting O3 or 3O2 units in the cluster structure, respectively. Copyright © 2008 John Wiley & Sons, Ltd.
Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges
Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H]5- obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H]5- ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug. Copyright © 2008 John Wiley & Sons, Ltd.
An algorithm for thorough background subtraction from high-resolution LC/MS data: application to the detection of troglitazone metabolites in rat plasma, bile, and urine
Interferences from biological matrices remain a major challenge to the in vivo detection of drug metabolites. For the last few decades, predicted metabolite masses and fragmentation patterns have been employed to aid in the detection of drug metabolites in liquid chromatography/mass spectrometry (LC/MS) data. Here we report the application of an accurate mass-based background-subtraction approach for comprehensive detection of metabolites formed in vivo using troglitazone as an example. A novel algorithm was applied to check all ions in the spectra of control scans within a specified time window around an analyte scan for potential background subtraction from that analyte spectrum. In this way, chromatographic fluctuations between control and analyte samples were dealt with, and background and matrix-related signals could be effectively subtracted from the data of the analyte sample. Using this algorithm with a ± 1.0 min control scan time window, a ± 10 ppm mass error tolerance, and respective predose samples as controls, troglitazone metabolites were reliably identified in rat plasma and bile samples. Identified metabolites included those reported in the literature as well as some that had not previously been reported, including a novel sulfate conjugate in bile. In combination with mass defect filtering, this algorithm also allowed for identification of troglitazone metabolites in rat urine samples. With a generic data acquisition method and a simple algorithm that requires no presumptions of metabolite masses or fragmentation patterns, this high-resolution LC/MS-based background-subtraction approach provides an efficient alternative for comprehensive metabolite identification in complex biological matrices. Copyright © 2008 John Wiley & Sons, Ltd.
Low-energy collision-induced fragmentation of negative ions derived from diesters of aliphatic dicarboxylic acids made with hydroxybenzoic acids
Diesters of ortho-hydroxybenzoic acid (salicylic acid) made with glutaric, adipic, and pimelic acids are the monomers of some potential drug candidates for aspirin patches. Collision-induced dissociation (CID) spectra of negative ion derived from these compounds show a 120-Da 'neutral loss' specific to the ortho isomers. In contrast, the anions derived from diesters of meta- and para-hydroxybenzoic acids show a 138-Da loss for an elimination of elements of hydroxybenzoic acid by a charge-remote mechanism. Deuterium labeling studies confirmed that the hydrogen atom transferred for hydroxybenzoic acid loss originates specifically from the [alpha] position of the dicarboxylic acid moiety. Although all spectra showed a peak at m/z 137, a charge-mediated process specific for the ortho compounds renders it the most prominent peak in the spectra of ortho compounds. Appropriate deuterium labeling experiments demonstrated that the hydrogen atom transferred for the formation of the m/z 137 ion in ortho compounds is specifically derived from the [alpha] position of the dicarboxylic acid moiety. Copyright © 2008 John Wiley & Sons, Ltd.
Insights into virus capsid assembly from non-covalent mass spectrometry
The assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self-assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti-viral therapeutics. It will also be important in bio-nanotechnology where there is a plethora of applications for such well-defined macromolecular complexes, including cell-specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non-covalently bound macromolecular complexes under near-physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Fragmentation patterns of newly isolated cassane butenolide diterpenes and differentiation of stereoisomer by tandem mass spectrometry
Different stereoisomers of active molecules often cause different physiological responses and hence pose a challenge for their identification. This study involves perceptive fragmentation behavior of newly isolated cassane butenolides, caesalpinolide A [1] and caesalpinolide B [2] (epimeric at the hemiketal position) by tandem MS. The electrospray ionization-mass spectrometry (ESI-MS)/collision-induced dissociation (CID; ESI-MS2 and ESI-IT-MSn) were investigated. The effect of orientations of hemiketal hydroxyl at C-12 was clearly observed in the mass spectrum. Tandem mass spectra of 1, 1A or 2, 2A show stereospecific fragmentation resulting in significant abundance dissimilarity of [MH - H2O]+ as well as differences in fragmentation pathway. Both of these pathways seem to be influenced by the stereochemistry of the molecule. The differentiation can be clearly visualized from the [M + H - H2O]+/[M + H]+ ratio of the two isomers where [beta]-isomer 2 was found to be five times higher than that of [alpha]-isomer 1 in full scan liquid chromatography-electrospray ionization mass spectrometry(LC-ESI-MS). In high-energy CID, the mass fingerprint of 1, 2, 1A, and 2A was found to be different from one anothers. Copyright © 2008 John Wiley & Sons, Ltd.
Determination of apparent decomposition threshold energies of lithium adducts of acylglycerols using tandem mass spectrometry and a novel derived effective reaction path length approach
Apparent decomposition threshold energies for the fragmentation pathways of lithiated acylglycerols were experimentally determined by collisional activation in a quadrupole-hexapole-quadrupole (QhQ) mass spectrometer. A previously developed 'derived effective reaction path length' approach for predicting bond dissociation energies (BDEs) of simple dissociations of electrostatic complexes such as alkali metal adducts (Li+), or halide adducts (Cl-) of acylglycerols, was extended to predict covalent bond apparent decomposition threshold energies of lithium adducts of a mono-acylglycerol, a 1,2-diacylglycerol, and a 1,3-diacylglycerol. The ability of the model to treat relatively large ionic systems (e.g. more than 100 atoms) represents a huge advantage of this approach. The model's calculated apparent decomposition threshold energies (Ea) are used in conjunction with the method of energy-resolved mass spectrometry, employing breakdown graphs, to give a more complete quantitative description of the fragmentation processes. Calculated Ea values allowed ranking of the 1,2-diacylglycerol as more reactive than the 1,3-diacylglycerol; the mono-acylglycerol was ranked the least reactive. The method was applied to the low molecular weight product ions generally associated with the hydrocarbon series CnH2n+1+, where two separate pathways are deduced as contributing to the production of the abundant m/z 81 fragment ion. The favored ranking of the neutral losses of fatty acyl substituents for the 1,2-diacylglycerol was determined as: loss of lithium fatty acetate > loss of fatty acid > loss of fatty acyl chain as ketene. For the 1,3-diacylglycerol, the descending order of ease of neutral loss was: loss of fatty acyl ketene > loss of lithium fatty acetate > loss of fatty acid. The results of this study demonstrate that the newly developed method is general in nature, and it can be used for the measurement of covalent bond decomposition threshold energies, as well as for the previously documented electrostatic (noncovalent) bond energies. Copyright © 2008 John Wiley & Sons, Ltd.
The ProteoMiner and the FortyNiners: Searching for gold nuggets in the proteomic arena
The present review covers modern aspects of combinatorial peptide ligand libraries (CPLL), as used to analyze the "low-abundance proteome" in association with mass spectrometry. First, the capturing properties of baits of different lengths (from single amino acid to hexa-peptides) are described to show that a plateau is rapidly reached above a tetra-peptide in length, thus confirming the validity of having adopted hexapeptides for the considered application. The mechanism of interaction with proteins from very complex proteomes and the ability to decrease the dynamic concentration range is demonstrated with the help of mass spectrometry analysis. Examples are given on how treatment with CPLLs dramatically improves the detectability of peptides in mass spectrometry analysis, permitting detection of a very large number of proteins as compared with control, untreated samples. The use of complementary libraries is discussed with the aim to discover additional low-abundance species that escaped the first library. A discussion on the possibility to discover extremely rare gene products, and the quantitative aspect of the technology when associated with mass spectrometry is also provided. Some insights on the applications for hidden, low-abundance biomarkers are also presented. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Accelerator mass spectrometry
In this overview the technique of accelerator mass spectrometry (AMS) and its use are described. AMS is a highly sensitive method of counting atoms. It is used to detect very low concentrations of natural isotopic abundances (typically in the range between 10-12 and 10-16) of both radionuclides and stable nuclides. The main advantages of AMS compared to conventional radiometric methods are the use of smaller samples (mg and even sub-mg size) and shorter measuring times (less than 1 hr). The equipment used for AMS is almost exclusively based on the electrostatic tandem accelerator, although some of the newest systems are based on a slightly different principle. Dedicated accelerators as well as older "nuclear physics machines" can be found in the 80 or so AMS laboratories in existence today. The most widely used isotope studied with AMS is 14C. Besides radiocarbon dating this isotope is used in climate studies, biomedicine applications and many other fields. More than 100,000 14C samples are measured per year. Other isotopes studied include 10Be, 26Al, 36Cl, 41Ca, 59Ni, 129I, U, and Pu. Although these measurements are important, the number of samples of these other isotopes measured each year is estimated to be less than 10% of the number of 14C samples. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Structural characterization of isoprenylated flavonoids from Kushen by electrospray ionization multistage tandem mass spectrometry
Eighteen isoprenylated flavonoids (8 flavanones, 3 flavanols, and 7 chalcones) isolated from Kushen or synthesized were studied by positive and negative ion electrospray ionization multistage tandem mass spectrometry (ESI-MSn). Plausible fragmentation patterns were obtained by comparing their MSn spectra with each other, which were further supported by high-resolution MS data and two model compounds. It was shown that the 2[prime]-OH group would make the C-ring of flavonoids studied more labile through a six-membered mechanism, resulting in base peaks of 1, 3A+ (positive mode) and 1, 4A- (negative mode). In addition, the 2[prime]-OH is also responsible for the neutral loss of water in (+)ESI/MS2 of flavanones. The neutral loss of water (or methanol) in (-)ESI/MS2 of flavanols was elucidated by a E2 elimination mechanism. Different relative abundances (RA) of 1, 3A+ and S+ in (+)ESI/MS2 spectra were used to discriminate flavanones with their open-ring products, chalcones, since the equilibrium for flavanonechalcone isomerization in ESI ion source could not be obtained in positive mode. Copyright © 2008 John Wiley & Sons, Ltd.
A tandem MS precursor-ion scan approach to identify variable covalent modification of albumin Cys34: a new tool for studying vascular carbonylation
We developed a liquid chromatography electrospray ionisation multi-stage mass spectrometry (LC-ESI-MS/MS) approach based on precursor-ion scanning and evaluated it to characterize the covalent modifications of Cys34 human serum albumin (HSA) caused by oxidative stress and reactive carbonyl species (RCS) adduction. HSA was isolated and digested enzymatically to generate a suitable-length peptide (LQQCPF) containing the modified tag residue. The resulting LQQCPF peptides were identified by LC-ESI-MS/MS in precursor-ion scan mode and further characterized in product-ion scan mode. The product ions for precursor-ion scanning were selected by studying the MS/MS fragmentation of a series of LQQCPF derivatives containing Cys34 modified with different [alpha],[beta]-unsaturated aldehydes and di and ketoaldehydes. We used a Boolean logic to enhance the specificity of the method: this reconstitutes a virtual current trace (vCT) showing the peaks in the three precursor-ion scans, marked by the same parent ion. The method was first evaluated to identify and characterize the Cys34 covalent adducts of HSA incubated with 4-hydroxy-hexenal, 4-hydroxy-trans-2-nonenal (HNE) and acrolein (ACR). Then we studied the Cys34 modification of human plasma incubated with mildly oxidized low-density lipoproteins (LDL), and the method easily identified the LQQCPF adducts with HNE and ACR. In other experiments, plasma was oxidized by 2,2'-azobis(2-amidinopropane) HCl (AAPH) or by Fe2+/H2O2. In both conditions, the sulfinic derivative of LQQCPF was identified and characterized, indicating that the method is suitable not only for studying RCS-modified albumin, but also to check the oxidative state of Cys34 as a marker of oxidative damage. Copyright © 2008 John Wiley & Sons, Ltd.
Formation of [b3 - 1 + cat]+ ions from metal-cationized tetrapeptides containing [beta]-alanine, [gamma]-aminobutyric acid or [epsiv]-aminocaproic acid residues
The presence and position of a single [beta]-alanine ([beta]A), [gamma]-aminobutyric acid ([gamma]ABu) or [epsiv]-aminocaproic acid (Cap) residue has been shown to have a significant influence on the formation of bn+ and yn+ product ions from a series of model, protonated peptides. In this study, we examined the effect of the same residues on the formation of analogous [b3 - 1 + cat]+ products from metal(Li+, Na+ and Ag+)-cationized peptides. The larger amino acids suppress formation of b3+ from protonated peptides with general sequence AAXG (where X = [beta]-alanine, [gamma]-aminobutyric acid or [epsiv]-aminocaproic acid), presumably because of the prohibitive effect of larger cyclic intermediates in the 'oxazolone' pathway. However, abundant [b3 - 1 + cat]+ products are generated from metal-cationized versions of AAXG. Using a group of deuterium-labeled and exchanged peptides, we found that formation of [b3 - 1 + cat]+ involves transfer of either amide or [alpha]-carbon position H atoms, and the tendency to transfer the atom from the [alpha]-carbon position increases with the size of the amino acid in position X. To account for the transfer of the H atom, a mechanism involving formation of a ketene product as [b3 - 1 + cat]+ is proposed. Copyright © 2008 John Wiley & Sons, Ltd.
In vivo evaluation and in vitro metabolism of leuprolide in mice - mass spectrometry-based biomarker measurement for efficacy and toxicity
The study of pharmacologically active peptides is central for the understanding of cancer and the development of novel therapeutic approaches. In this context, both qualitative and quantitative determination of bioactive peptides in biological fluids/tissues and their effect on endogenous factors (e.g. hormones) are of great importance. A mass spectrometry-based approach was developed and applied towards the measurement of leuprolide, a peptide drug for the treatment of prostate cancer, in mouse plasma. High-pressure liquid chromatography coupled to a hybrid quadrupole linear ion trap (QqLIT) mass spectrometer, a platform that combines the benefits of triple QqLIT instruments, was employed for the study. Using the described methodology, we established that picomolar concentrations of leuprolide could be measured in mouse plasma (limit of quantification of 0.1 ng/ml). In order to optimize pharmacokinetic properties of analogs of leuprolide, a facile in vivo mouse model was developed and leuprolide concentrations were determined in mouse plasma following intraperitoneal administration. In the same animal model, we demonstrated the versatility of the described MS-based approach by the determination of plasma concentrations of testosterone, an established biomarker for the treatment of prostate cancer. Following dosing with leuprolide, circulating testosterone was increased significantly in comparison to vehicle-treated mice. Finally, in vitro metabolism of leuprolide was evaluated by incubation of leuprolide with mouse kidney membranes, followed by identification of major metabolites by MS. Such studies provide the framework for future evaluation of novel leuprolide analogs with potential therapeutic advantages. Copyright © 2008 John Wiley & Sons, Ltd.
A fully validated isotope dilution HPLC-MS/MS method for the simultaneous determination of succinylcholine and succinylmonocholine in serum and urine samples
A high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) method for the simultaneous detection of succinylcholine (SUX) and its metabolite succinylmonocholine (SMC) in serum and urine is presented. For internal standardization using isotope dilution, the deuterated compounds SUX-d18 and SMC-d3 were employed. Full validation was performed according to international guidelines. Solid-phase extraction (SPE) of acidified samples was accomplished using Strata-X polymeric reversed phase cartridges together with heptafluorobutyric acid (HFBA) as ion-pairing reagent. Separation was achieved within 13 min on a Phenomenex Synergi Hydro RP C18 column (4 µm, 150 × 2 mm) using a gradient of 5 mM ammonium formate buffer pH 3.5 and acetonitrile.To ensure the method's applicability in forensic as well as clinical toxicology, the specific demands of both research fields were taken into account, and the method was thus validated for a low and high concentration range. For both serum and urine as sample matrix, the validation revealed good intraday and interday precisions, consistently ranging below 15% for the lowest and below 10% for elevated concentrations. Accuracy was likewise good and never exceeded 10%. Extraction recovery was excellent, ranging between 88.1 and 103.9% for SUX and SMC in both tested matrices. Matrix effects were significant, the otherwise optimized extraction and detection methods, however, allowed for a very satisfactory sensitivity of the described method: For serum, the limits of detection and quantitation were determined to be 1.9 and 6.0 ng/ml for SUX, as well as 2.5 and 8.6 ng/ml for SMC, respectively; for urine, the corresponding values were established to be 1.4 and 4.0 ng/ml (SUX), as well as 1.5 and 4.9 ng/ml (SMC).The presented method was successfully applied to authentic samples of two forensic cases investigated in the institute of forensic medicine in Bonn, allowing the diagnosis of SUX intoxications. Copyright © 2008 John Wiley & Sons, Ltd.
Mass spectrometric studies of potent inhibitors of farnesyl protein transferase - detection of pentameric noncovalent complexes
Farnesyl protein transferase (FPT) inhibition is an interesting and promising approach to noncytotoxic anticancer therapy. Research in this area has resulted in several orally active compounds that are in clinical trials. Electrospray ionization (ESI) time-of-flight mass spectrometry (TOF-MS) was used for the direct detection of a 95 182 Da pentameric noncovalent complex of [alpha]/[beta] subunits of FPT containing Zn, farnesyl pyrophosphate (FPP) and SCH 66336, a compound currently undergoing phase III clinical trials as an anticancer agent. It was noted that the desalting of protein samples was an important factor in the detection of the complex. This study demonstrated that the presence of FPP in the system was necessary for the detection of the FPT-inhibitor complex. No pentameric complex was detected in the spectrum when the experiment was carried out in the absence of the FPP. An indirect approach was also applied to confirm the noncovalent binding of SCH 66336 to FPT by the use of an off-line size exclusion chromatography followed by liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) for the detection of the inhibitor. Copyright © 2008 John Wiley & Sons, Ltd.
Mass spectrometric analysis of illicit drugs in wastewater and surface water
Residues of illicit drugs have been recently found in urban wastewater and surface water. Their levels reflect the amount of drugs collectively excreted by consumers and can therefore be used to estimate drug abuse. An overview of the most widely used illicit drugs and of the analytical methods used for their detection in wastewater and surface water is presented here. Solid-phase extraction and high performance liquid chromatography-tandem mass spectrometry are the techniques that have been used for these investigations. Instrumental conditions and fragmentation patterns of illicit drugs and their metabolites are described. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 378-394, 2008
Proteomics in gram-negative bacterial outer membrane vesicles
Gram-negative bacteria constitutively secrete outer membrane vesicles (OMVs) into the extracellular milieu. Recent research in this area has revealed that OMVs may act as intercellular communicasomes in polyspecies communities by enhancing bacterial survival and pathogenesis in hosts. However, the mechanisms of vesicle formation and the pathophysiological roles of OMVs have not been clearly defined. While it is obvious that mass spectrometry-based proteomics offers great opportunities for improving our knowledge of bacterial OMVs, limited proteomic data are available for OMVs. The present review aims to give an overview of the previous biochemical, biological, and proteomic studies in the emerging field of bacterial OMVs, and to give future directions for high-throughput and comparative proteomic studies of OMVs that originate from diverse Gram-negative bacteria under various environmental conditions. This article will hopefully stimulate further efforts to construct a comprehensive proteome database of bacterial OMVs that will help us not only to elucidate the biogenesis and functions of OMVs but also to develop diagnostic tools, vaccines, and antibiotics effective against pathogenic bacteria. © 2008 Wiley Periodicals, Inc., Mass Spec Rev
Computational view of surface based organic mass spectrometry
Surface based mass spectrometric approaches fill an important niche in the mass analysis portfolio of tools. The particular niche depends on both the underlying physics and chemistry of molecule ejection as well as experimental characteristics. In this article, we use molecular dynamics computer simulations to elucidate the fundamental processes giving rise to ejection of organic molecules in atomic and cluster secondary ion mass spectrometry (SIMS), massive cluster impact (MCI) mass spectrometry, and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. This review is aimed at graduate students and experimental researchers. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 289-315, 2008
Rapid screening and characterization of drug metabolites using a multiple ion monitoring-dependent MS/MS acquisition method on a hybrid triple quadrupole-linear ion trap mass spectrometer
A novel LC/MS/MS method that uses multiple ion monitoring (MIM) as a survey scan to trigger the acquisition of enhanced product ions (EPI) on a hybrid quadrupole-linear ion trap mass spectrometer (Q TRAP) was developed for drug metabolite identification. In the MIM experiment, multiple predicted metabolite ions were monitored in both Q1 and Q3. The collision energy in Q2 was set to a low value to minimize fragmentation. Results from analyzing ritonavir metabolites in rat hepatocytes demonstrate that MIM-EPI was capable of targeting a larger number of metabolites regardless of their fragmentation and retained sensitivity and duty cycle similar to multiple reaction monitoring (MRM)-EPI. MIM-based scanning methods were shown to be particularly useful in several applications. First, MIM-EPI enabled the sensitive detection and MS/MS acquisition of up to 100 predicted metabolites. Second, MIM-MRM-EPI was better than MRM-EPI in the analysis of metabolites that undergo either predictable or unpredictable fragmentation pathways. Finally, a combination of MIM-EPI and full-scan MS (EMS), as an alternative to EMS-EPI, was well suited for routine in vitro metabolite profiling. Overall, MIM-EPI significantly enhanced the metabolite identification capability of the hybrid triple quadrupole-linear ion trap LC/MS. Copyright © 2008 John Wiley & Sons, Ltd.
The mass spectral analysis of isolated hops A-type proanthocyanidins by electrospray ionization tandem mass spectrometry
Comprehensive mass spectral fragmentation patterns have been established for sequencing chromatographically isolated A-type proanthocyanidins (PAs) using electrospray ionization tandem mass spectrometry (ESI-MSn) in the positive ion mode similar to those used for sequencing previously reported B-type PAs. Sequence-identifying fragmentations for A-type PAs include heterocyclic ring fission (HRF), retro-Diels-Alder (RDA) fission, benzofuran-forming (BFF) fission, and quinone methide (QM) fission. There is commonality in fragmentation patterns between A-type and B-type PAs, but distinguishing features in the mass spectral patterns between the two classes include 2-Da mass differences in the pseudo molecular ions, the propensity for the A-type PAs to undergo QM fissions and yield bis-quinoid ions as opposed to mono-quinoid ions in the upper unit of the sequence, and the reluctance of A-type linkages to undergo RDA, BFF, and BFF/H2O fissions from the upper unit. The positions of one or more A-type (C2 [rarr] O [rarr] C7[prime]) ether linkages have been located in sequences of PAs ranging in chain lengths of two to five monomer units using ESI-MSn data. Using the fragmentation information from ESI-MSn experiments, a total of 17 PAs were structurally sequenced by systematic real time ESI-MSn. Among them ten A-type and six B-type hop PAs are reported here for the first time. Copyright © 2008 John Wiley & Sons, Ltd.
Characterization of the pH-dependent dissociation of a multimeric metalloprotein Streptomyces rubiginosus xylose isomerase by ESI FT-ICR mass spectrometry
We report an analysis of the pH-dependent dissociation of a multimeric metalloprotein, xylose isomerase from Streptomyces rubiginosus (XI), by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Xylose isomerases are industrially significant enzymes that catalyze interconversion of aldose and ketose sugars. XI is biologically active as a [sim]173-kDa tetrameric complex, comprised of four identical [sim]43-kDa subunits and eight metal cations, unequivocally identified as the Mg2+ cations in this work. ESI FT-ICR mass spectra of XI measured in the pH range of 3.0-6.9 indicated that the dissociation of the intact holo-tetramer is initiated by the loss of all eight Mg2+ cations at pH [le]5.0, followed by step-by-step dissociation of the remaining apo-tetramer to trimers, dimers and monomers. In addition, a [sim]346-kDa protein octamer was detected at pH 6.9. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitation of cardioexcitatory Asn-D-Trp-Phe-NH2 diastereomers in Aplysia's central nervous system by nanoscale liquid chromatography-tandem mass spectrometry
A tripeptide, Asn-D-Trp-Phe-NH2 (NdWFa) that contains a D-amino acid residue (i.e. D-tryptophan) was previously identified in Aplysia's central nervous system (CNS) and found to be cadioexcitatory. However, the occurrence of its diastereomers including NWFa, theoretically the precursor of NdWFa, remains largely unknown. In this work, a nanoscale liquid chromatographic/tandem mass spectrometric (nano-LC-MS/MS) method was developed for a sensitive determination of the diastereomers of NWFa. Resolution of the diastereomers including NWFa, NdWFa, NWdFa, and dNWFa was achieved on capillary columns packed with C18 silica particles with an MS detection-friendly mobile phase consisting of water, acetonitrile, and formic acid. Columns of different internal diameters (IDs) ranging from 75 to 250 µm were evaluated to achieve the best sensitivity. With the use of a 75 µm ID column integrated with a nanoelectrospray emitter, the method had limits of detection (LOD) of 0.21 nM (or 0.49 pg on column, 5 µl injected) NdWFa in tissue homogenate (S/N = 3). The five major ganglia in Aplysia californica's CNS (i.e. buccal, cerebral, abdominal, plural, and pedal) were analyzed. NdWFa was detected only in abdominal ganglion at the ng/g tissue level. Further, its diastereomer, NWFa, was also detected for the first time and also only in abdominal ganglion at a significantly lower level. The levels of both NWFa and NdWFa varied from animal to animal in the range from 0 to 81 ng/g tissue. Copyright © 2008 John Wiley & Sons, Ltd.
Direct injection LC/ESI-MS horse urine analysis for the quantification and identification of threshold substances for doping control. I. Determination of hydrocortisone
Two simple and rapid LC/MS methods with direct injection analysis were developed and validated for the quantification and identification of hydrocortisone in equine urine using the same sample preparation but different mass spectrometric systems: ion trap mass spectrometry (IT-MS) and time-of-flight mass spectrometry (TOF-MS). The main advantage of the proposed methodology is the minimal sample preparation procedure, as particle-free diluted urine samples were directly injected into both LC/MS systems. Desonide was used as internal standard (IS). The linear range was 0.25-2.5 µg ml-1 for both methods. Matrix effects were evaluated by preparing and analyzing calibration curves in water solutions and different horse urine samples. A great variation of the signal both for hydrocortisone and the internal standard was observed in different matrices. To overcome matrix effects, the unavailability of blank matrix and the excessive cost of the isotopically labeled internal standard, standard additions calibration method was applied. This work is an exploration of the performance of the standard additions approach in a method where neither nonisotopic internal standards nor extensive sample preparation is utilized and no blank matrix is available. The relative standard deviations of intra and interday analysis of hydrocortisone in horse urine were lower than 10.2 and 5.4%, respectively, for the LC/IT-MS method and lower than 8.4 and 4.4%, respectively, for the LC/TOF-MS method. Accuracy (bias percentage) was less than 9.7% for both methods. Copyright © 2008 John Wiley & Sons, Ltd.
Proteome analysis of non-model plants: A challenging but powerful approach
Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 354-377, 2008
A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: In vivo characterization and structure/function relationships
Mass spectrometry has evolved in recent years to a well-accepted and increasingly important complementary technique in molecular and structural biology. Here we review the many contributions mass spectrometry based studies have made in recent years in our understanding of the important cyclic nucleotide activated protein kinase A (PKA) and protein kinase G (PKG). We both describe the characterization of kinase isozymes, substrate phosphorylation, binding partners and post-translational modifications by proteomics based methodologies as well as their structural and functional properties as revealed by native mass spectrometry, H/D exchange MS and ion mobility. Combining all these mass spectrometry based data with other biophysical and biochemical data has been of great help to unravel the intricate regulation of kinase function in the cell in all its magnificent complexity. © 2008 Wiley Periodicals, Inc. Mass Spec Rev 27: 331-353, 2008
Multiresidue method for the analysis of more than 140 pesticide residues in fruits and vegetables by gas chromatography coupled to triple quadrupole mass spectrometry
A new multiresidue method has been developed and validated for the determination of more than 140 pesticide residues in cucumber and orange by gas chromatography coupled to triple quadrupole mass spectrometry (GC-QqQ-MS/MS) in a single run of 25.50 min. The triple quadrupole (QqQ) analyzer simultaneously operated in the selected reaction monitoring (SRM) and selected ion monitoring (SIM) modes, acquiring two or three transitions per compound. Samples were extracted by the application of a single-phase extraction of 10 g of sample with acetonitrile containing 1% of acetic acid, followed by a liquid-liquid partition formed by the addition of 4 g of MgSO4 and 1 g of NaOAc. A dispersive solid-phase extraction (D-SPE) with primary secondary amine (PSA) was applied to clean up the extracts. A final concentration step was included in order to increase sensitivity in the instrumental analysis. The method was properly validated in each matrix in a wide dynamic range (10-400 µg kg-1): this work relies on a new quantification strategy by the use of two calibration curves to increase the dynamic range, which permitted reduction of sample dilutions and increase in sample throughput. Recovery was studied at three concentration levels (11.5, 50.0, and 150.0 µg kg-1), yielding values in the range 70-110% with precision values, expressed as relative standard deviation (RSD), lower than 20 and 25% for the intraday and interday precision, respectively. Limits of quantification (LOQs) were established at 10 µg kg-1, the lowest maximum residue level (MRL) value set by the European Union in vegetables. The method was successfully applied to the analysis of pesticide residues in real samples from the southeastern Spain. Copyright © 2008 John Wiley & Sons, Ltd.
Liquid and gas chromatography coupled to isotope ratio mass spectrometry for the determination of 13C-valine isotopic ratios in complex biological samples
On-line gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) is commonly used to measure isotopic ratios at natural abundance as well as for tracer studies in nutritional and medical research. However, high-precision 13C isotopic enrichment can also be measured by liquid chromatography-isotope ratio mass spectrometry (LC-IRMS). Indeed, LC-IRMS can be used, as shown by the new method reported here, to obtain a baseline separation and to measure 13C isotopic enrichment of underivatised amino acids (Asp, Thr-Ser, Glu, Pro, Gly, Ala, Cys and Val). In case of Val, at natural abundance, the SD([delta]13C) reported with this method was found to be below 1[permil] . Another key feature of the new LC-IRMS method reported in this paper is the comparison of the LC-IRMS approach with the conventional GC-C-IRMS determination. To perform this comparative study, isotopic enrichments were measured from underivatised Val and its N(O, S)-ethoxycarbonyl ethyl ester derivative. Between 0.0 and 1.0 molar percent excess (MPE) ([delta]13C = - 12.3 to 150.8[permil]), the calculated root-mean-square (rms) of SD was 0.38 and 0.46[permil] and the calculated rms of accuracy was 0.023 and 0.005 MPE, respectively, for GC-C-IRMS and LC-IRMS. Both systems measured accurately low isotopic enrichments (0.002 atom percent excess (APE)) with an SD (APE) of 0.0004. To correlate the relative ([delta]13C) and absolute (atom%, APE and MPE) isotopic enrichment of Val measured by the GC-C-IRMS and LC-IRMS devices, mathematical equations showing the slope and intercept of the curves were established and validated with experimental data between 0.0 to 2.3 MPE. Finally, both GC-C-IRMS and LC-IRMS instruments were also used to assess isotopic enrichment of protein-bound 13C-Val in tibial epiphysis in a tracer study performed in rats. Isotopic enrichments measured by LC-IRMS and GC-C-IRMS were not statistically different (p > 0.05). The results of this work indicate that the LC-IRMS was successful for high-precision 13C isotopic measurements in tracer studies giving 13C isotopic enrichment similar to the GC-C-IRMS but without the step of GC derivatisation. Therefore, for clinical studies requiring high-precision isotopic measurement, the LC-IRMS is the method of choice to measure the isotopic ratio. Copyright © 2008 John Wiley & Sons, Ltd.
Ion chemistry in germane/fluorocompounds gaseous mixtures: a mass spectrometric and theoretical study
The ion-molecule reactions occurring in GeH4/NF3, GeH4/SF6, and GeH4/SiF4 gaseous mixtures have been investigated by ion trap mass spectrometry and ab initio calculations. While the NFx+ (x = 1-3) react with GeH4 mainly by the exothermic charge transfer, the open-shell Ge+ and GeH2+ undergo the efficient F-atom abstraction from NF3 and form GeF+ and F[bond]GeH2+ as the only ionic products. The mechanisms of these two processes are quite similar and involve the formation of the fluorine-coordinated complexes Ge[bond]F[bond]NF2+ and H2Ge[bond]F[bond]NF2+, their subsequent crossing to the significantly more stable isomers FGe[bond]NF2+ and F[bond]GeH2[bond]NF2+, and the eventual dissociation of these ions into GeF+ (or F[bond]GeH2+) and NF2. The closed-shell GeH+ and GeH3+
