Showing papers in "Mass Spectrometry Reviews in 2001"

Practical implications of some recent studies in electrospray ionization fundamentals.

Abstract: In accomplishing successful electrospray ionization analyses, it is imperative to have an understanding of the effects of variables such as analyte structure, instrumental parameters, and solution composition. Here, we review some fundamental studies of the ESI process that are relevant to these issues. We discuss how analyte chargeability and surface activity are related to ESI response, and how accessible parameters such as nonpolar surface area and reversed phase HPLC retention time can be used to predict relative ESI response. Also presented is a description of how derivitizing agents can be used to maximize or enable ESI response by improving the chargeability or hydrophobicity of ESI analytes. Limiting factors in the ESI calibration curve are discussed. At high concentrations, these factors include droplet surface area and excess charge concentration, whereas at low concentrations ion transmission becomes an issue, and chemical interference can also be limiting. Stable and reproducible non-pneumatic ESI operation depends on the ability to balance a number of parameters, including applied voltage and solution surface tension, flow rate, and conductivity. We discuss how changing these parameters can shift the mode of ESI operation from stable to unstable, and how current-voltage curves can be used to characterize the mode of ESI operation. Finally, the characteristics of the ideal ESI solvent, including surface tension and conductivity requirements, are discussed. Analysis in the positive ion mode can be accomplished with acidified methanol/water solutions, but negative ion mode analysis necessitates special constituents that suppress corona discharge and facilitate the production of stable negative ions.

Characterization of intact microorganisms by MALDI mass spectrometry.

Abstract: The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review. Instrumentation, sample collection, sample preparation, and algorithms for data analysis are summarized. Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry.

MALDI-TOF mass spectrometry of bacteria.

Abstract: The development of MALDI-TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed. The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins. More surprising was the observation that MALDI-TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification. Versatility and the rapidity of analysis led to the rapid development of a number of MALDI-TOF methods involving bacteria. Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level. The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI-TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real-time methods for the characterization of bacteria.

Perspectives for mass spectrometry and functional proteomics.

Abstract: Permission to reproduce this table online was not granted by the copyright holder. Readers are kindly asked to refer to the printed version.

Molecular recognition and supramolecular chemistry in the gas phase

Abstract: Supramolecular chemistry, in particular, the fields of molecular recognition and self-assembly, profit much from the development of soft ionization techniques and advanced methods for mass analysis and gas-phase chemistry. Vice versa, weakly bonded architectures and host-guest complexes represent a veritable challenge for the mass spectrometrist, leading to further development of methods and techniques. This review describes the state-of-the-art in this field, and includes topics such as the effects of solvation on meta binding to crown ethers, chiral discrimination of guests by chiral hosts, the elucidation of the secondary structure of self assembled complexes, and the mechanistic pathways of self assembly or the fragmentations of supramolecular complexes in the gas phase.

Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins

Abstract: I. Introduction 61 II. Binding of Small Molecules to DNA 62 A. Covalent Binding 62 B. Reversible (Noncovalent) DNA-Binding Agents 65 III. DNA-Metal Ion Complexes 67 A. Platinum Complexes 70 B. Other Metal Ions 73 IV. DNA-Protein Complexes 74 A. Introduction 74 B. ESI-MS of DNA-Protein Complexes 76 C. ESI-MS Analysis of Proteolytic Products of DNA-Protein Complexes 79 D. ESI-MS of Ternary DNA-Protein-Ligand Complexes 80 V. Conclusions 80 Abbreviations 81 References 81 --Interactions of DNA with drugs, metal ions, and proteins are important in a wide variety of biological processes. With the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), mass spectrometry (MS) is now a well-established tool for the characterization of the primary structures of biopolymers. The gentle nature of the ESI process, however, means that ESI-MS is also finding application for the study of noncovalent and other fragile biomolecular complexes. We outline here the progress, to date, in the use of ESI-MS for the study of noncovalent drug-DNA and protein-DNA complexes together with strategies that can be employed to examine the binding of small molecules and metal complexes to DNA. In the case of covalent complexes with DNA, sequence information can be derived from ESI-MS used in conjunction with tandem mass spectrometry (MS/MS) and/or enzymatic digestion. MS/MS can also be used to probe the relative binding affinities of drugs that bind to DNA via noncovalent interactions. Overall, the work in this area, to date has demonstrated that ESI-MS and MS/MS will prove to be valuable complements to other structural methods, offering advantages in terms of speed, specificity, and sensitivity. (c) 2001 John Wiley & Sons, Inc.

Computational chemistry: a useful (sometimes mandatory) tool in mass spectrometry studies.

Abstract: In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.

Analysis of nucleic acids by on‐line liquid chromatography–Mass spectrometry

Abstract: The numerous problems posed by modern biochemistry, biology, and medicine, as well as the growing significance of genetic engineering require the application of fast and reliable methods of utmost sensitivity and selectivity for the analysis of nucleic acids. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) represent established analytical techniques for the characterization and structural elucidation of single- and double-stranded nucleic acids, ranging in size from a few nucleotides to several thousand base pairs. Although both techniques are independently applicable for nucleic acid analysis, the on-line hyphenation significantly enhances their potential for the robust and fully automable routine analysis of minute amounts of biological samples. Among the various chromatographic and mass spectrometric modes available in principle, ion-pair reversed-phase HPLC and electrospray ionization mass spectrometry (ESI-MS) have been shown to be the most suitable for the direct interfacing of liquid chromatography (LC) and MS. Instrumental setup, as well as chromatographic and mass spectrometric experimental conditions, need to be carefully selected in order to maximize the performance of the hyphenated analytical system. Applications of HPLC-ESI-MS include the characterization of oligodeoxynucleotides synthesized by solid-phase synthesis, the analysis of antisense oligodeoxynucleotides, oligonucleotide metabolites, and DNA adducts, the analysis of genomic segments specifically amplified by the polymerase chain reaction (PCR), the characterization of ribonucleic acids, the sizing of double-stranded DNA restriction fragments, the genotyping of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), the detection of mutations in nucleic acid sequences, and the sequencing of nucleic acids.

Radical approaches to probe protein structure, folding, and interactions by mass spectrometry.

Abstract: I. Introduction 388 II. Case for Radicals 389 III. Radiation and Discharge Radical Sources 390 IV. Reaction Products: Nature of Amino Acid Modifications 391 V. Protein Integrity Versus Damage 392 VI. Reaction Kinetics and Protein Structure Elucidation 394 VII. Protein Folding: Equilibrium and Time-Resolved Studies 395 VIII. Protein Complexes and Assemblies 397 IX. Conclusions 398 Acknowledgments 399 References 399 This review describes mass spectrometry-based strategies and investigations to determine protein structure, folding dynamics, and protein-protein interactions in solution through the use of radical reagents. The radicals are generated in high flux within microseconds from synchrotron radiation and discharge sources, and react with proteins on time scales that are less than those often attributed to structural reorganization and folding. The oxygen-based radicals generated in aqueous solution react with proteins to effect limited oxidation at specific amino acids throughout the sequence of the protein. The extent of oxidation at these residue markers is highly influenced by the accessibility of the reaction site to the bulk solvent. The extent of oxidation allows protection levels to be measured based on the degree to which a reaction occurs. A map of a protein's three-dimensional structure is subsequently assembled as in a footprinting experiment. Protein solutions that contain various concentrations of substrates that either promote or disrupt dynamic structural transitions can be investigated to facilitate site-specific equilibrium and time-resolved studies of protein folding. The radical-based strategies can also be employed in the study of protein–protein interactions to provide a new avenue for investigating protein complexes and assemblies with high structural resolution. The urea-induced unfolding of apomyoglobin and the binding of gelsolin to actin are among the systems presented to illustrate the approach. © 2002 Wiley Periodicals, Inc., Mass Spec Rev 20:388–401, 2001; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10013

New trends in the application of electron ionization to liquid chromatography—mass spectrometry interfacing

Abstract: Permission to reproduce this table online was not granted by the copyright holder. Readers are kindly asked to refer to the printed version. Two recent approaches for coupling capillary scale liquid chromatography and electron ionization mass spectrometry are reviewed and discussed. The first one, Cap-EI, is the latest evolution of the micro-scale particle beam interface, in which the nebulizer has been optimized to overcome the limitations of the former approach, in terms of sensitivity and linearity. It can be easily hosted in pre-existing instruments without major modifications and can use helium and the less-expensive nitrogen to generate library-matchable electron ionization spectra. The second one is a miniaturized interface for nano- and micro-HPLC, in which the interfacing process takes place into a suitably modified ion source. Because the eluate from the column is completely transferred into the ion source for ionization, superior sensitivity, linearity, and reproducibility are obtained. No signs of chemical ionization are observed at flow rates up to 1.5 μL/min. These two interfaces demonstrate that electron ionization can be successfully used for the analysis of small—medium molecules of various polarities, and also at the trace level. The possibility to record library-matchable electron ionization spectra offers the analyst a powerful tool that can be particularly useful in real-world applications.© 2001 John Wiley & Sons, Inc., Mass Spec Rev 20: 88–104, 2001

Monitoring 2-D gel-induced modifications of proteins by MALDI-TOF mass spectrometry.

Abstract: I. Introduction 121 II. Protein Alkylation by Acrylamide and Its N-Substituted Monomers 122 III. Protein Alkylation by Free Immobiline Chemicals 125 IV. Site of Reaction 127 V. Probing Protein Unfolding Through the Monitoring of Cys Alkylation 129 VI. Protein Reactions with a Number of Gel Electrophoresis Crosslinkers 130 VII. Do Such Modifications Manifest Themselves in Real-Life Analyses? 134 VIII. How Does Sample Preparation for 2-D Gels Influence Certain Modifications? 136 IX. What Are the Consequences of a Poor Sample Alkylation? 136 X. Conclusions 138 Acknowledgments 139 References 139 In addition to more than 200 endogenously produced post-translational modifications, a detailed analysis of 2-D gel-separated proteins must also consider other modifications that a protein can experience during various steps of its separation. This review describes the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to investigate some of these modifications, which can originate during sample preparation and/or during the separation phase. The analyses described were mostly conducted at pH 9–9.5, and yielded reliable information on stable adduct formation that involved protein-bound amino acids and a number of gel components, including acrylamide derivatives, gel cross-linkers, and Immobiline chemicals. The –SH group of Cys was found to be the prime target of such adducts; however, longer reaction times revealed the involvement of the e-NH2 of Lys. The same analysis revealed that the failure to achieve full reduction/alkylation prior to any electrophoretic step could result in protein–protein interaction, which could lead to a number of spurious spots in the final 2-D map. The implications of these modifications on the MS analysis in particular and on proteome research in general are discussed. © 2001 John Wiley & Sons, Inc., Mass Spec Rev 20:121–141, 2001

Compound-specific isotope analysis of the organic constituents in carbonaceous chondrites.

Abstract: The carbonaceous chondrite meteorites contain evidence of the formation of the solar system, part of which is present within organic matter. In recent years, compound-specific isotope analysis (CSIA) has been useful in deciphering this complex record. The current published data set provides an insight into the source environments and reaction mechanisms that have contributed to the final state of the organic constituents in carbonaceous chondrites. This review summarises the CSIA data and related key interpretations.

Proteins in vacuo: denaturing and folding mechanisms studied with computer-simulated molecular dynamics.

Abstract: Proteins in vacuo: Denaturing and folding mechanisms studied with computersimulated molecular dynamics

Base‐induced 1,4‐elimination:Insights from theory and mass spectrometry*

Abstract: Experimental and theoretical studies on gas-phase base-induced 1,4-elimination reactions are summarized and discussed. The emphasis is on the synergy that is achieved by combining the complementary data from mass spectrometry and theoretical chemistry. The scope and applications of 1,4-eliminations are discussed and compared with other elementary reactions; e.g., 1,2-elimination and aliphatic (S(N)2) and allylic (S(N)2') nucleophilic substitution. Furthermore, the syn versus anti stereochemistry of 1,4-elimination reactions and the effect of E versus Z stereochemistry of the substrate are examined. Particular attention is paid to the mechanistic nature of 1,4-elimination, i.e., E2 or E1cb, as well as special features such as the single-well E2 and E1cb mechanism. Also, new results from density functional theory computations (BP86/TZ2P) are presented.

Molecular orbital treatment of gas-phase ion molecule collision rates: Reactive and nonreactive collisions

Abstract: I. Introduction 142 II. Reaction Efficiency 144 III. Ion Polar-Molecule Collisions 145 IV. Momentum-Transfer Ion-Molecule Collisions 146 V. Summary 151 Acknowledgments 151 References 151 This paper reviews some applications of quantum mechanical models to ion-molecule collision processes, and presents a new theoretical approach to ion mobilities of isobaric ions. Reactive ion-molecule collisions have been successfully modeled, using perturbation molecular orbital (PMO) theory, and ab initio quantum mechanical models. In ion polar-molecule collisions, the Stark effect exerts a controlling influence on the collision rate. The average dipole orientation for an ion polar-molecule collision is exactly zero. The instantaneous dipole orientation to the ion-molecule axis in these collisions is not zero. The instantaneous angle between the dipole and the ion-molecule axis, Θ, increases as the distance between the ion and molecule, r, decreases. The Stark effect couples collisional angular momentum of the ion-molecule complex and rotational angular momentum of the molecule. Conversion of collisional angular momentum to rotational angular momentum causes the rotation of the molecule to increase as the ion and molecule approach each other. Changes in Θ directly follow the changes in rotational angular momentum for the molecule. In momentum transfer ion-molecule collisions in gases, the energy difference between the frontier orbitals of the collision pair is such that a first-order perturbation model is not appropriate. An approximate second-order PMO equation for the reduced mobility of ions in non-polar gases, Ko PMO, is presented and used to analyze data from the literature. Ion mobility is linearly related to Ko PMO, a function of the ion-molecule electronic potential, ΔEIM, and the reduced mass, μIM, for the ion bath-gas interaction. The electronic states of first-row transition metal ions separated by ion-mobility in helium have been assigned on the basis of their reduced mobilities. © 2001 John Wiley & Sons, Inc., Mass Spec Rev 20:142–152, 2001