Single drop microextraction coupled with matrix-assisted laser desorption/ionization mass spectrometry for rapid and direct analysis of hydrophobic peptides from biological samples in high salt solution

Single drop microextraction (SDME) coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been applied for direct analysis of hydrophobic peptides (valinomycin and gramicidin D) from biological samples (urine and plasma) in high salt solution. The optimal conditions such as selection of extraction solvent, stirring rate, extraction time, effect of salt concentration and matrix-to-analyte ratio were investigated. The limits of detection (LODs) were found to be 73 nM to 170 nM for valinomycin and 96 nM to 5.5 µM for gramicidin D in high salt solution (1.7 M of NaCl) in MALDI-MS. The current approach can enhance the LODs by 11-320-fold for gramicidin D analysis in water, urine and plasma in high salt solution. Furthermore, the current approach has been successfully demonstrated for real-world sample analysis (β-carotene from carrots) by MALDI-MS. The current approach is a rapid, simple and efficient clean-up platform for direct analysis of hydrophobic molecules in biological samples from high salt solution.

Application of probe electrospray to direct ambient analysis of biological samples

Recently, we have developed probe electrospray ionization (PESI) that uses a solid needle. In this system, the probe needle moves up and down along the vertical axis by a motor-driven system. At the highest position of the probe needle, electrospray is generated by applying a high voltage. In this study, we applied PESI directly to biological samples such as urine, mouse brain, mouse liver, salmon egg, and fruits (orange, banana, etc.). Strong ion signals for almost all the samples were obtained. The amount of liquid sample picked up by the needle is as small as pL or less, making PESI a promising non-invasive technique for detecting biomolecules in living systems such as cells. Therefore, PESI may be useful as a versatile and ready-to-use semi-online analytical tool in the fields of medicine, pharmaceuticals, agriculture, food science, etc.

Self-assembled-monolayer-modified silicon substrate to enhance the sensitivity of peptide detection for AP-MALDI mass spectrometry

A self-assembled-monolayer-modified silicon substrate was successfully used to enhance the sensitivity of peptide detection for atmospheric pressure-matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI/MS). The effect of surface modification of silicon wafer samples with NH(2) and OH functional groups was investigated. In addition, solvent effects for the preparation of modified NH(2)-functionalized surfaces were examined. The sensitivities for the two peptides were significantly improved, increasing between 12 and 160 times, for bradykinin and gramicidin, respectively, on an NH(2)-modified silicon surface prepared in toluene, over that on a conventional gold substrate. The limits of detection (LODs) for bradykinin and gramicidin using the conventional gold substrate in AP-MALDI/MS experiments were > 0.011 microM and 110 microM, respectively. Using our SAM approach, the LODs for bradykinin and gramicidin in AP-MALDI/MS can be improved to 0.93 nM and 0.33 microM, respectively. This SAM approach for AP-MALDI/MS is simple and sensitive, and can be used for high-throughput analysis.

TOF-SIMS analysis using C60. Effect of impact energy on yield and damage

C60 has been shown to give increased sputter yields and, hence, secondary ions when used as a primary particle in SIMS analysis. In addition, for many samples, there is also a reduction in damage accumulation following continued bombardment with the ion beam. In this paper, we report a study of the impact energy (up to 120 keV) of C60 on the secondary ion yield from a number of samples with consideration of any variation in yield response over mass ranges up to m/z 2000. Although increased impact energy is expected to produce a corresponding increase in sputter yield/rate, it is important to investigate any increase in sample damage with increasing energy and, hence, efficiency of the ion beams. On our test samples including a metal, along with organic samples, there is a general increase in secondary ion yield of high-mass species with increasing impact energy. A corresponding reduction in the formation of low-mass fragments is also observed. Depth profiling of organic samples demonstrates that when using C60, there does not appear to be any increase in damage evident in the mass spectra as the impact energy is increased.

Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide

Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.

Direct analysis of gramicidin double helices using packed column supercritical fluid chromatography

Direct analysis of the monomeric and four double helical dimeric conformations of gramicidin has been achieved using packed column supercritical fluid chromatography (pSFC). Using a PRP-1 polymeric column and typical conditions of 40 degrees C column temperature, 25 MPa column pressure, and 35% n-pentanol modifier addition, all of the gramicidin conformers were readily separated. To evaluate the method, the dynamic characteristics of the monomer and dimer species were monitored as a function of solvent type, incubation time, solvent temperature, and initial concentration. The findings agree with those previously obtained by other methods but also yield new information about the relative amounts of two closely related dimers (species 1 and 2) as well as the simultaneous changes in the full dimer/monomer distribution. Results indicate that the developed pSFC method can be an informative complimentary tool for readily monitoring changes in the full profile of gramicidin species present in different environments.

Specific photodissociation of peptides with multi-stage mass spectrometry

We report collision-induced dissociation (CID) and laser-induced dissociation (LID) performed at different wavelengths between 220 and 280 nm of the peptides leucine-enkephalin (protonated) and gramicidin A (sodiated). Hydrogen-atom losses and side-chain cleavages were observed in LID experiments. These losses depend on the laser wavelength and lead to the formation of radical ions. The fragmentations of these radicals, which are not observed in CID experiments, were investigated in multi-stage mass spectrometry experiments.

Influence of protein flexibility on the electrostatic energy landscape in gramicidin A

We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.

Electrospray ionization-mass spectrometry and tandem mass spectrometry reveal self-association and metal-ion binding of hydrophobic peptides: a study of the gramicidin dimer

Gramicidin is a membrane pentadecapeptide that acts as a channel, allowing the passage of monovalent metal ions and assisting in bacterial cell death. The active form is a noncovalently bound dimer. One means to study the self-assembly of this peptide has been to compare the state of the peptide in various solvents ranging from hydrophilic (e.g., trifluoroethanol) to hydrophobic (e.g., n-propanol). In this article, we report the use of electrospray mass spectrometry to study the self-association of gramicidin in various organic and mixed solvents that are introduced directly into the mass spectrometer. The dimer (both homo and hetero) can survive the introduction into the gas phase, and the amount in the gas phase increases with the decreasing dielectric constant of the solvent, reflecting solution-phase behavior. Tandem mass spectrometry data reveal that the stability of dimer in the gas phase decreases with increasing metal ion size, strongly suggesting that the metal ion binds inside the dimer between the monomers.

Ion mobility-mass spectrometry applied to cyclic peptide analysis: conformational preferences of gramicidin S and linear analogs in the gas phase

In this paper, we present an investigation of the gas-phase structural differences between cyclic and linear peptide ions by matrix-assisted laser desorption ionization-ion mobility-mass spectrometry. Specifically, data is shown for gramicidin S (cyclo-VOLFPVOLFP where phenylalanines are D rather than L-type amino acids and the O designates the non-standard amino acid ornithine) and five linear gramicidin S analogues. Results are interpreted as evidence for a beta-sheet (or beta-hairpin) conformational preference in both linear-protonated and sodiated-cyclic gramicidin S gas-phase peptides, and a preference for the protonated-cyclic peptide to adopt a collapsed, random coil-type conformation. A comparison with solution-phase circular dichroism measurements is performed, and structures similar to those observed in the gas phase appear to be favored in low-dielectric solvents such as 2,2,2-triflouroethanol. The utility of ion mobility-mass spectrometry (IM-MS) as a means of rapidly distinguishing between linear and cyclic peptide forms in also discussed.

Orthogonal time-of-flight secondary ion mass spectrometric analysis of peptides using large gold clusters as primary ions

Secondary ion mass spectrometry (SIMS) for biomolecular analysis is greatly enhanced by the instrumental combination of orthogonal extraction time-of-flight mass spectrometry with massive gold cluster primary ion bombardment. Precursor peptide molecular ion yield enhancements of 1000, and signal-to-noise improvements of up to 20, were measured by comparing SIMS spectra obtained using Au(+) and massive Au(400) (4+) cluster primary ion bombardment of neat films of the neuropeptide fragment dynorphin 1-7. Remarkably low damage cross-sections were also measured from dynorphin 1-7 and gramicidin S during prolonged bombardment with 40 keV Au(400) (4+). For gramicidin S, the molecular ion yield increases slightly as a function of Au(400) (4+) beam fluence up to at least 2 x 10(13) Au(400) (4+)/cm(2). This is in marked contrast to the rapid decrease observed when bombarding with ions such as Au(5) (+) and Au(9) (+). When gramicidin S is impinged with Au(5) (+), the molecular ion yield decreases by a factor of 10 after a fluence of only 8 x 10(12) ions/cm(2). Comparison of these damage cross-sections implies that minimal surface damage occurs during prolonged Au(400) (4+) bombardment. Several practical analytical implications are drawn from these observations.

Improved precision and accuracy for high-performance liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometric exact mass measurement of small molecules from the simultaneous and controlled introduction of internal calibrants via a second electrospray nebuliser

The use of a second electrospray nebuliser has proved to be highly successful for exact mass measurement during high-performance liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICRMS). Much improved accuracy and precision of mass measurement were afforded by the introduction of the internal calibration solution, thus overcoming space charge issues due to the lack of control over relative ion abundances of the species eluting from the HPLC column. Further, issues of suppression of ionisation, observed when using a T-piece method, are addressed and this simple system has significant benefits over other more elaborate approaches providing data that compares very favourably with these other approaches. The technique is robust, flexible and transferable and can be used in conjunction with HPLC, infusion or flow injection analysis (FIA) to provide constant internal calibration signals to allow routine, accurate and precise mass measurements to be recorded.

Two-dimensional microfabricated sources for nanoelectrospray

The idea of a novel two-dimensional (2D) nanoelectrospray ionization emitter tip with the shape of a nib is explored here. This novel planar design is studied as an alternative to the needle-like standard emitter tips that suffer from a lack of reproducibility and robustness and from an inherent incompatibility with high-throughput analysis. The composition of the micro-nib sources is analogous to the working of a simple fountain pen, with a liquid reservoir linked to a micro-nib tip from which the sample is electrosprayed via a capillary slot. The micro-nib prototypes described here were fabricated using microtechnology techniques and using the epoxy-based negative photoresist SU-8. The resulting free-standing micro-nib structure was supported by a silicon wafer. We present here two series of such micro-nib sources, the latter series exhibiting improved characteristics such as a 8 micro m source width of the nib tip. They were tested in mass spectrometry experiments on an ion trap mass spectrometer (LCQ Deca XP+, Thermo Finnigan) using standard peptide samples having concentrations down to 1 micro M and with a high voltage (HV) supply around 1 kV for the second series of micro-nib sources. In addition to the stability of the spray, the obtained mass spectra showed the reliability of these sources for peptide analysis; the signal of the spectra was as intense and the signal-to-noise ratio (S/N) as high as that obtained with the use of standard emitter tips.

Hyphenation of liquid chromatography to ion trap mass spectrometry to identify minor components in polypeptide antibiotics

The application of liquid chromatography-ion trap mass spectrometry for the characterization of linear and cyclic polypeptide antibiotics was investigated. The aim was on-line identification of impurities in those antibiotic complexes without recourse to time-consuming isolation and purification procedures. Hyphenated techniques, such as liquid chromatography coupled to mass spectrometry, are ideally suited for this purpose. Characterization was performed with an ion trap mass spectrometer offering MS(n) capability; this enables more structural information to be obtained. Liquid chromatography in combination with ion trap mass spectrometry was successfully applied for the characterization of impurities in gramicidin, polymyxin B, polymyxin E, and bacitracin and the study of the degradation products of polymyxins B and E.

Application of Molecular Beam Deflection Time-of-Flight Mass Spectrometry to Peptide Analysis

The application of molecular beam deflection time-of-flight mass spectrometry (MBD-TOFMS) to peptide identification is described. The technique permits a simultaneous measurement of molecular mass and electric dipole susceptibility. The mass and susceptibility are not strongly correlated, and the results can be presented as a two-dimensional map. The susceptibility provides a useful way to disperse isobaric and isomeric peptides, and at least for small peptides, the susceptibility is significantly different for different amino acid sequences. Results for peptides in the mass range 1000-2300 Da show that the mass and susceptibility lead to a higher identification score than mass spectra alone.

Size-exclusion high-performance liquid chromatography in the study of the autoassociating antibiotic gramicidin A in micellar milieu

Gramicidin A (gA) is a polypeptide antibiotic which forms dimeric channels specific for monovalent cations in biological membranes. It is a polymorphic molecule that adopts several different conformations, double-stranded (ds) helical dimers (pore conformation) and single-stranded beta-helical dimers (channel conformation). This study investigated the conformational adaptability of gramicidin A when incorporated into micelles as membrane-mimetic model system. Taking advantage of our reported, versatile, size-exclusion high-performance liquid chromatography (SE-HPLC) strategy that allows the separation of double-stranded dimers and monomers, we have quantitatively characterized the conformational transition undergone by the peptide in the micellar milieu. The importance of both hydrophobic/hydrophilic moieties of the amphipaths in the stabilization of concrete conformational species is demonstrated using detergents with different hydrocarbon chain length and/or polar head. SE-HPLC is a valuable, rapid, accurate technique for the structural characterization of hydrophobic autoassociating peptides that work in lipid environments such as biological membranes.

A quantitative model of ultraviolet matrix-assisted laser desorption/ionization including analyte ion generation

A quantitative model of ionization in ultraviolet matrix-assisted laser desorption/ionization (Knochenmuss, R. J. Mass Spectrom. 2002, 37, 867) is extended to include secondary ion-molecule reactions. Matrix-to-analyte charge-transfer reaction kinetics are described by a hard-sphere Arrhenius expression. The activation energy is derived from the reaction exoergicity using a nonlinear free energy relationship. The approach is applied to the specific case of proton-transfer reactions. With no adjustable parameters, the model correctly predicts the existence and characteristics of the matrix and analyte suppression effects, the shapes of the two-pulse time-delayed yield curves, and the dependence of analyte yields on laser fluence, molecular weight, relative concentrations, and reaction exoergicity.

Gramicidin A interaction at a dioleoyl phosphatidylcholine monolayer on a mercury drop electrode

A biosensor where the sensing surface is a fluid dioleyl phosphatidylcholine monolayer (DOPC) deposited on a mercury drop was used. The lipid monolayer was held in 0.1 M NaCl and a concentration of gramicidin A in the range 0-12 nM was used. Electrochemical impedance spectroscopy in the frequency range 0.1-65 kHz was employed to investigate how the defect-free monolayer responds to interactions of gramicidin A in solution. The data was analyzed both with multivariate data analysis and classical electrochemical methods. The principal component analysis of the resulting impedance spectra gave a linear dependence on the concentration of gramicidin A. An increasing permittivity was observed in the low-frequency regime with increasing concentration of gramicidin A in solution.

Micro-electrospray with stainless steel emitters

The physical processes underlying micro-electrospray (micro-ES) performance were investigated using a stainless steel (SS) emitter with a blunt tip. Sheathless micro-ES could be generated at a blunt SS tip without any tapering or sanding if ESI conditions were optimized. The Taylor cone was found to shrink around the inner diameter of the SS tubing, which permitted a low flow rate of 150 nL/min for sheathless microspray on the blunt tip (100 microm i.d. x 400 microm o.d.). It is believed that the wettability and/or hydrophobicity of SS tips are responsible for their micro-ES performance. The outlet orifice was further nipped to reduce the size of the spray cone and limit the flow rate to 50-150 nL/min, resulting in peptide detection down to attomole quantities consumed per spectrum. The SS emitter was also integrated into a polymethylmethacrylate microchip and demonstrated satisfactory performance in the analysis and identification of a myoglobin digest.

Ion dispersion near parallel wire grids in orthogonal acceleration time-of-flight mass spectrometry: predicting the effect of the approach angle on resolution

Ions experience small deflections in the vicinity of grids in accelerators and ion mirrors in time-of-flight (TOF) mass spectrometers. Recent experiments with an orthogonal acceleration (oa) TOF instrument have verified that the effect can significantly degrade resolution when ions approach grids at an angle deviating from 90 degrees. The phenomenon becomes significant only when ions have components of velocity at right angles to the wires of the grids. A model is presented in this study to predict this phenomenon for parallel wire grids. The fractional energy spread of ions (calculated in the static TOF-spectrometer frame of reference) scales directly with the approach angle of ions to the grid (as measured from normal approach). The energy spread also scales with the range of angles that is a consequence of the focusing effect in each gap between the wires of the grid. The equations imply that closely spaced parallel wire grids are best for deployment in oa-TOF systems where non-zero approach angles are unavoidable. Such grids are relatively impractical to manufacture and support but rectangular repeat cell grids with relatively few wires at right angles to the source axis are shown experimentally to introduce minimal energy spread. When these grids are rotated by 90 degrees, the resolution measured in a Q-TOF spectrometer is degraded in approximate agreement with the parallel wire model. A practical implication of this work is that grid transmissions in oa-TOF systems may be significantly increased without loss of resolution. Improvements of approximately 200% (V-mode) and approximately 400% (W-mode) in ion transmission were obtained in this study without compromising resolution. This was achieved with approximately 73% transmission grids and greater potential improvements in transmission are being realised since this study with approximately 89% transmission grids having similar geometry.

A new technique for unbiased external ion accumulation in a quadrupole two-dimensional ion trap for electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

External ion accumulation in a two-dimensional (2D) multipole trap has been shown to increase the sensitivity, dynamic range and duty cycle of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. However, it is important that trapped ions be detected without significant bias at longer accumulation times in the external 2D multipole trap. With increasing ion accumulation time pronounced m/z discrimination was observed when trapping ions in an accumulation quadrupole. In this work we show that superimposing lower rf-amplitude dipolar excitation over the main rf-field in the accumulation quadrupole results in disruption of the m/z discrimination and can potentially be used to achieve unbiased external ion accumulation with FTICR.

Analysis of lipophilic peptides and therapeutic drugs: on-line-nonaqueous capillary electrophoresis-mass spectrometry

This minireview addresses the usefulness of nonaqueous capillary electrophoresis-mass spectrometry (NACE-MS), mainly in the analysis of lipophilic peptides such as gramicidin S and bacitracin, and therapeutic drugs such as pyrazoloacridine, the H2-antagonist mifentidine, tamoxifen, and their metabolites. The beneficial effects of NACE-MS in typical bioanalytical applications are analyzed case by case. A suitable and widely applicable NACE-MS analysis is identified, which is an electrolyte buffer containing ammonium acetate (5-50 mM) and/or acetic acid (up to 100 mM) with varying composition of organic solvents. Either acetonitrile or methanol or a mixture of the two are mostly utilized in the nonaqueous media. Primary considerations in developing NACE-MS are also discussed.

An ion funnel interface for improved ion focusing and sensitivity using electrospray ionization mass spectrometry

To improve upon the already impressive sensitivity achievable with electrospray ionization sources, a novel electrohydrodynamic ion funnel interface has been developed and implemented with a triple-quadrupole mass spectrometer. The ion funnel interface effectively consists of a series of ring electrodes of increasingly small internal diameters to which rf and dc electric potentials are coapplied. In the 1-10-Torr pressure range, the electric fields cause the collisionally damped ions to be more effectively focused and transmitted as a collimated ion beam. This paper describes the ion funnel design and presents an evaluation of its performance using a triple-quadrupole mass spectrometer. Ion transmission and m/z discriminating parameters (resulting in both effective low- and high-m/z cutoffs) are presented based upon both ion current measurements and mass spectra. Electrospray ionization mass spectra of selected protein solutions demonstrated well over 1 order of magnitude increase in signal relative to that of the instrument operated in its standard (inlet capillary-skimmer) configuration under similar conditions. The present results suggest that it will be feasible to realize close to 100% ion transmission efficiency for analytically relevant ions through the electrospray ionization interface and into the mass analyzer.

Separation of amino acid and peptide stereoisomers by nonionic micelle-mediated capillary electrophoresis after chiral derivatization

Enantiomers of amino acids and peptides were derivatized with a fluorescent chiral reagent, 4-(3-isothiocyanatopyrrolidinl-yl)-7-nitro-2,1,3-benzoxadiazole [R-(-)- or S-(+)-NBD-PyNCS] and the resulting diastereomeric derivatives separated by capillary electrophoresis (CE). The CE running buffer consisted of 25 mM acetate buffer (pH 4) and 10 mM of the nonionic surfactant Triton X-100. The excitation maximum of NBD-PyNCS at 480 nm matches the major Ar-ion emission line at 488 nm allowing sensitive laser-induced fluorescence detection with limits of detection around 50 nM. D-Proline and D-aspartate spiked (at 10(-4) M and 10(-5) M concentrations, respectively) into complex biological matrices (rabbit serum and homogenate of Aplysia californica buccal ganglion) are detected without matrix interferences. This method has also been applied to the determination of D- and L-amino acid residues in peptides after acid hydrolysis. Results from the chiral analysis of the naturally-occurring peptide, gramicidin D, are shown.

Liquid chromatographic analysis of a formulation containing polymyxin, gramicidin and neomycin

The development of a liquid chromatographic essay system for the stability study of a formulation containing polymyxin, gramicidin and neomycin is described. For the determination of each group of antibiotics, poly(styrenedivinylbenzene) is used as the stationary phase. The mobile phase for the determination of polymyxin consists of an aqueous solution containing 7 g l-1 of sodium sulfate, 50 ml l-1 of 1 M phosphoric acid and 160 ml l-1 of acetonitrile. UV detection is performed at 215 nm. An aqueous solution containing 70 g l-1 of sodium sulfate, 1.4 g l-1 of sodium octanesulfonate and 50 ml l-1 of 0.2 M phosphate buffer pH 3.0 is used as the mobile phase for the determination of neomycin. Since neomycin has no UV-absorbing chromophore, pulsed electrochemical detection is chosen to determine neomycin. For each method, the influence of the different chromatographic parameters on the separation, the selectivity towards the other active compounds and the excipients, the repeatability and the linearity were investigated. The stability of the formulation was examined at 0, 6 and 12 months.

Enhancement of the molecular ion yield in plasma desorption mass spectrometry using explosive matrices

The working hypothesis of this study was that the chemical energy of matrix material may be released, although only on a microscale, under MeV ion bombardment and may assist ejection of large intact bioorganic molecules. To test the hypothesis, the performance of several common explosives, as matrices in plasma desorption mass spectrometry, was compared to the standard matrix, nitrocellulose (NC), which is also a high explosive. Two explosives, RDX and HMX, were found to be new, effective matrices for peptides and proteins. While the performance of RDX was comparable with that of nitrocellulose, HMX gave a superior molecular ion yield and a higher average charge state of desorbed molecular ions compared with NC. Noth RDX and HMX have a similar chemical composition and structure, although the latter is a more powerful explosive. The measured total ion yield allows the conclusion that the increase in the amount of ejected material, due to the chemical energy release in high explosives under MeV ion bombardment, is limited, perhaps to a factor of 2 to 3. The fact that not all tested explosives gave molecular ions from peptides and proteins suggests that other factors, such as gas-phase chemistry, may play a significant role in molecular ion formation.

Effects of alanine and glycine substitution for tryptophan on the heterogeneity of gramicidin A analogs in micelles

The effects of alanine and glycine substitution for tryptophan upon the species heterogeneity of gramicidin A analogs incorporated into SDS micelles have been investigated. The sequential replacement of the four tryptophan residues in gramicidin A at positions 15, 13, 11, and 9 with glycine showed that there was no detectable effect at position 15 but increasing heterogeneity of species in the micelles proceeding toward the interior of the micelle at position 9. The replacement of tryptophan at positions 15 and 9 with alanine was found to produce more species heterogeneity than found with glycine substitution at the same positions. An increase in the SDS concentration reduces the number of different species present in micelles. With the Gly-11, Gly-13, and Gly-15 analogs, the increase in SDS concentration results in the formation of a single species; however, for the Gly-9, Ala-9, and Ala-15 analogs, heterogeneity remains.

Effects of fusogenic and DNA-binding amphiphilic compounds on the receptor-mediated gene transfer into hepatic cells by asialofetuin-labeled liposomes

Effects of fusogenic and DNA-binding amphiphilic compounds on the receptor-mediated gene transfer using asialofetuin-labeled liposomes (AF-liposomes) were examined with HepG2 cells and rat hepatocytes in primary culture. AF-liposomes were sufficiently taken up by both types of cells through the asialoglycoprotein receptor-mediated endocytosis. In HepG2 cells, bacterial beta-galactosidase (beta-Gal) gene expression was observed by transfection using AF-liposomes encapsulating plasmid pCMV beta DNA (AF-liposome-pCMV beta). By addition of dioleoylphosphatidylethanolamine (DOPE) to the liposomal lipid composition (AF-liposome(DOPE)-pCMV beta), the transfection efficiency was clearly increased. The effects of DOPE were more conspicuous in the presence of chloroquine in the medium throughout the transfection. When pCMV beta complexed with gramicidin S (pCMV beta (GrS)) was encapsulated (AF-liposome(DOPE)-pCMV beta (GrS) and was transfected to HepG2 cells, an significantly high beta-Gal activity in the cells was observed as compared with that in the cells transfected with AF-liposome(DOPE)-pCMV beta. No effects of GrS were found in the transfection using AF-non-labeled control liposomes. In primary culture of rat hepatocytes, no beta-Gal gene expression was observed even though AF-liposome(DOPE)-pCMV beta was introduced into the cells prepared from adult rats. However, following the transfection with AF-liposome(DOPE)-pCMV beta, the beta-Gal activity was expressed in the cells from immature rats cultured in the medium supplemented with epidermal growth factor and insulin, and the transfection efficiency was 2-fold higher than that transfected with pCMV beta encapsulated in AF-non-labeled control liposomes. By the complex formation of pCMV beta with GrS, the transfection efficiency of AF-liposome(DOPE)-pCMV beta (GrS) increased according to the increase of GrS in the complex. It was shown that AF-liposome(DOPE)-pCMV beta (GrS) did efficiently introduce and express beta-Gal gene in both HepG2 cells and primary hepatocytes in the receptor mediated manner.

Quadrupole ion trap mass spectrometry

A number of other features of ITMS systems that will enhance their ability to analyze biological macromolecules are worth mentioning. As has already been demonstrated for ESI/quadrupole, ESI/magnetic sector, and ESI/FTICR systems, the capability of inducing fragmentation of the ESI-generated multiply charged ions of biological macromolecules in the capillary/skimmer region of the ESI source and subsequently selectively analyzing fragments can also be carried out with the QITMS, as we have demonstrated using bovine serum albumin (data not shown). The ability to carry out chemical reactions on biological macromolecules inside the QITMS has been demonstrated by McCluckey et al. by showing that the introduction of a pulse of volatile base, such as diethylamine, can result in proton removal from multiply charged protein ions, resulting in species with lower charge states. The application of the technique of deuterium exchange of active hydrogens on peptides to simplify the interpretation of MS/MS sequencing experiments can be implemented for ESI/QITMS. Carrying out such exchange inside the ITMS may also be possible, with resulting analytical advantages. Reports of a hybrid QITMS-TOF system, which was operated with either ESI or MALDI methodology, and which demonstrated low femtomolar sensitivity with higher resolution of the TOF analyzer because of ion injection of essentially monoenergetic ions from the QITMS into the TOF, illustrate additional uses of the QITMS. The reverse combination (e.g., ESI/TOF/QITMS or MALDI/TOF/QITMS) could afford preselection of ions for even higher performance in the QITMS, because space charging (loss of performance such as resolution because of too much charge in close proximity in the ion trap) would be minimized. Opportunities for the application of QITMS technology for the analysis of biological macromolecules abound, including ultrahigh-sensitivity protein sequencing using specifically derivatized amino acids released by Edman chemistry; rapid sequencing of MHC-associated antigenic peptides of variable length (approximately nonamers for the MHC I complexes to > dodecamers for the MHC II complexes), which are available in only very low amounts (femtomole/attomole) and in very complex mixtures (5000-10,000 species) of closely related peptide structures; ultrahigh-sensitivity analysis of peptides and proteins directly in vivo using microelectrospray; direct analysis of metal ion binding to peptides and proteins and analysis of noncovalent interactions, including conformation; and possible analysis of plasmid DNA, as has been suggested by ESI ionization of a 2-MDa DNA species. In summary, the ability of the QITMS to interface to key separations systems such as HPLC and HPCE through the critical ionization techniques of ESI and MALDI, coupled with the high mass range, high mass resolution, high sensitivity, high-efficiency CID, and MS capabilities of this device, will provide an astonishing array of cost-effective capabilities for the qualitative and quantitative analysis of biological macromolecules.

Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing

Characterization and verification of the structures of large biomolecules with high-resolution tandem Fourier transform mass spectrometry with electrospray ionization is critically dependent on the technique used to fragment the multiply charged ions produced. Infrared multiphoton dissociation (IRMPD) of ionized proteins as large as carbonic anhydrase (29 kDa) yields fragment information similar to, but with valuable additions to, that of other dissociation techniques. IRMPD yields product ions on-axis, providing efficient dissociation in further stages; MS3 of ubiquitin (8.6 kDa) yields 11 new sequence ions. Optimum irradiation times for protein ion dissociation vary by more than a factor of 6, with times for oligonucleotides far lower, possibly due to photon resonance with a P-O stretching frequency. IRMPD provides far greater selectivity than collisionally activated dissociation and also appears to yield much less mass discrimination and to dissociate much more stable ions. A technique to remove product ions on formation from the laser beam should improve the present efficiencies of 30-80%.

MS/MS with high detection efficiency and mass resolving power for product ions in Fourier transform ion cyclotron resonance mass spectrometry

We present a new FT-ICR method for MS/MS of trapped ions. Parent ions isolated in the source trap of a dual-trap FT-ICR/MS instrument are subjected to off-resonance dipolar excitation to promote collision-induced dissociation (CID), while product ions are simultaneously axialized by broad-band azimuthal quadrupolar excitation in the presence of argon collision gas. In this way, radial diffusional loss of product ions is greatly reduced; moreover, the axialized product ions may then be efficiently transferred to the analyzer trap for high-resolution detection. Significant improvements in FT-ICR detection efficiency, mass resolving power (m/delta m > or = 20,000 at m/z < or = 1000), and mass accuracy (< or = 50 ppm for peptide fragments of m/z < or = 1000) are demonstrated for CID product ions of the cyclic peptide, gramicidin S.

Thin gold film-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry of biomolecules

A new thin gold film-assisted (TGFA) laser desorption/ionization (LDI) technique has been combined with Fourier transform ion cyclotron resonance (FT-ICR) high-resolution mass analysis. A thermally labile organic sample is coated onto a thin gold film deposited on a glass plate and desorbed and ionized by Nd:YAG laser irradiation. The wavelength for maximum light absorption may be tuned by varying the thickness of the metal film; e.g., a 10-nm-thick gold film absorbs maximally near the Nd:YAG fundamental wavelength (1064 nm). A key advantage of the method is the stability of the gold film, which facilitates deposition of samples from any of a variety of solvent systems. Coupled with recently introduced quadrupolar excitation and collisional cooling for ion axialization, TGFA-LDI FT-ICR mass spectra provide high sensitivity (e.g., 100-fmol single-shot detection limit and mass resolving power, m/delta m approximately 113,000, for (M+K)+ ions from gramicidin S at m/z 1180).

Tandem time-of-flight mass spectrometer

A compact, laser desorption tandem time-of-flight mass spectrometer is described. The instrument incorporates two dual-stage reflectron analyzers and a collision region for producing product ions by collision-induced dissociation. Selection of ions of a particular mass is accomplished by deflection of ions from stable trajectory angles entering the second reflectron, while the use of a pulsed valve for introduction of the collision gas obviates the need for differential pumping of the collision region. Initial results are presented, as well as a discussion for optimizing the performance of tandem time-of-flight instruments.

Deuterium NMR of Val1...(2-2H)Ala3...gramicidin A in oriented DMPC bilayers

Deuterium NMR is used to study the selectively labeled Val1...(2-2H)Ala3...gramicidin A molecule to investigate the structure and dynamics of the C alpha-2H bond in the Ala3 residue of gramicidin. Val1...(2-2H)Ala3...gramicidin A is synthesized, purified, and characterized and then incorporated into oriented bilayers of dimyristoylphosphatidylcholine sandwiched between glass coverslips. Phosphorus NMR line shapes obtained from this sample are consistent with the presence of the bilayer phase and indicate that no nonbilayer phases are present in significant amounts. Deuterium NMR line shapes obtained from this sample indicate that the motional axis of the gramicidin Ala3 residue is parallel to the coverslip normal, that the distribution of motional axis orientations has a width of 2 degrees, and that only one major conformational and dynamical state of the Ala3 C alpha-2H bond is observed on the NMR time scale. Furthermore, the Ala3 C alpha-2H bond angle relative to the motional axis is 19-20 degrees if fast axial rotation is assumed to be the only motion present but is less than or equal to 19-20 degrees in the absence of such an assumption. This result indicates that various double-stranded, helical dimer models are very unlikely to represent the structure of gramicidin in the sample studied but that the single-stranded, beta 6.3 helical dimer models are consistent with the experimental data. However, a definitive distinction between the left-handed, single-stranded, beta 6.3 helical dimer model and the right-handed, single-stranded, beta 6.3 helical dimer model cannot be made on the basis of the experimental data obtained in this study.

New high-performance liquid chromatography-based methodology for monitoring the conformational transitions of self-associating hydrophobic peptides, incorporated into liposomes

A new high-performance size-exclusion chromatographic strategy is reported for the analysis of the hydrophobic self-associating peptide gramicidin A, incorporated into artificial phospholipid vesicles (liposomes). The method is based on the direct injection of a few microlitres of the gramicidin A-containing liposome suspension into the column, which is eluted with a non-polar solvent, such as tetrahydrofuran. The type and amount of information which can be derived from this methodology have been evaluated. Using this chromatographic approach, a correlation has been unambiguously shown to exist between the organization of the peptide in the vesicles and a number of variables involved in the method of preparation of liposomes. Finally, a gramicidin A conformational transition has been monitored in the phospholipid vesicles which proved to be dependent on the class of phospholipid present in the liposome.

Dielectric relaxation spectroscopy on dimyristoylphosphatidylcholine-packaged gramicidin A

The complex permittivities of aqueous suspensions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and of DMPC packaged gramicidin A' (DMPC-GA) have been determined over the frequency range of 1 MHz to 1 GHz and the temperature range of 0-60 degrees C. A dielectric relaxation/loss has been observed at about 66 MHz for the DMPC suspension (30 degrees C) and at about 57 MHz for the DMPC-GA suspension (30 degrees C). This dielectric relaxation/loss has been attributed to the rotational mobility of the zwitterionic group of DMPC. The temperature dependence (from 60 degrees C to 0 degrees C) of this dispersion/absorption process of the DMPC suspension indicates a sharp reduction of the dielectric relaxation at about 20 degrees C. This dielectric change is related to the conversions of shape and structure of bilayer aggregates. This sharp reduction of the dielectric relaxation disappears or broadens when GA is incorporated into the DMPC aqueous suspension. The interpretation of these results is that the GA addition into the DMPC aqueous suspension induces a small decrease of the rotational mobility of the zwitterionic group above the lipid phase transition, and a small increase of the rotational mobility of the zwitterionic group below the lipid phase transition.

[Spatial structure of gramicidin A in organic solvents. 1H-NMR analysis of conformation heterogeneity in ethanol]

Structural features of double helices formed by polypeptides with alternating L- and D-amino acid residues were analysed. It was found that the map of short distances (less than 4 A) between protons of the two backbones is unique for each double helix type and even its fragment implies unambiguously parameters of the helix (i.e. parallel or antiparallel, handedness, pitch of helix, relative shift of polypeptide chains). By analysis of two-dimensional 1H-NMR spectra (COSY, RELSY, HOHAHA, NOESY), proton resonances of [Val1]gramicidin A (GA) in the ethanol solution were assigned. The results obtained show that the solution contains five stable conformations of GA in comparable concentrations. Monomer of GA is in a random coil conformation. Specific maps of short interproton distances for the other four species (1-4) were obtained by means of two dimensional nuclear Overhauser effect spectroscopy. The maps as well as spin-spin couplings of the H-NC alpha-H protons and solvent accessibilities of the individual amide groups correspond to four types of double helices pi pi LD 5,6 with 5.6 residues per turn. The double helices are related to the Veatch species 1-4 of GA. Species 1 and 2 are left-handed parallel double helices increase increase pi pi LD 5,6 with different relative shift of polypeptide chains. Species 3 is a left-handed antiparallel double helix increase decrease pi pi LD 5,6 and species 4 is a right-handed parallel double helix increase increase LD 5,6. In the dimers helices are fixed by the maximum number (28) of interbackbone hydrogen bonds NH...O = C possible for these structures. Species 1, 3 and 4 have C2 symmetry axes. Relationship between gramicidin A spatial structures induced by various media is discussed.

Improvements in instrumentation for thermospray operation on a magnetic sector mass spectrometer

Changes in the design of a thermospray liquid chromatography-mass spectrometry ion source can be made to improve the sensitivity towards solute related ions and therefore extend the practical utility of the complete system. The addition of a discharge ionization facility provides much greater scope for gradient elution analyses and forms the basis of a method which offers increased structural information. All of these changes are illustrated by practical examples.

A Raman spectroscopic study on the interaction of an ion-channel protein with a phospholipid in a model membrane system (gramicidin A/L-alpha-lysophosphatidylcholine)

The interaction of the ion channel polypeptide gramicidin A with the L-alpha-lysophosphatidylcholine micelles in a membrane state association (approximative molar ratio 1:9) was investigated by Raman spectroscopy. Studies were carried out over the spectral ranges of 700-1700 cm-1 and 2800-3100 cm-1 at 10 degrees C. The Raman spectrum of L-alpha-lysophosphatidylcholine micelles indicated a disordered structure of the lipid acyl chains by the high intensities of the gauche conformation vibrations. Changing from the micellar phase to the membrane state of association with gramicidin A, the intensities of all-trans stretching modes increased whereas the intensities of gauche conformation vibrations decreased, reflecting the emergence of ordered lipid chains. Hydrophobic interactions between the acyl chains and the polypeptide side chain residues were demonstrated. The absence of modifications in intensities of the very strong tryptophan vibrations in the complex spectrum indicated that, if the tryptophan-stacking interactions suggested by some authors exist, they are very weak ones.

The structure of crystalline and membrane-bound gramicidin A by vibrational analysis

The results of normal mode calculations on the beta 4.4, beta 6.3, beta 5.6, and beta 7.2 structures of gramicidin A are compared with infrared and Raman spectra of crystalline native, crystalline Cs+-bound, and vesicle-bound gramicidin A. The observed frequencies and frequency splittings are in good agreement with an assignment of beta 5.6, beta 7.2, and beta 6.3 structures, respectively, to the gramicidin A molecules in the above three systems.

Anomalous exchange kinetics of peptide amide protons in aqueous solutions

Reports concerning anomalous rates of exchange of some amides in oxytocin, alumichrome, and gramicidin S are reexamined through systematic analysis of the exchange data as a function of pH and primary structure. It is shown that such an analysis can provide useful information on secondary structure when the degree of hydrogen bonding to both the NH undergoing exchange and the neighboring carbonyl group are taken into consideration.

Phospholipids containing photoactivable groups in studies of biological membranes

Photoactivable carbene precursors, aryl diazirines and trifluorodiazopropionates, were incorporated synthetically into the omega-positions of fatty acids, which were used to synthesize phospholipids. Extensive intermolecular C--H insertion reactions were demonstrated by photolysis of liposomes prepared from the above phospholipids. Structural analysis of the cross-linked products showed that the predominant sites of cross-linking were in the expected positions within the bilayer. Studies on the topography of a number of membrane proteins using the above phospholipids were initiated. Cross-linking of the photoactivable phospholipids to membrane-embedded proteins, glycophorin A, cytochrome b5, and gramicidin A, was demonstrated.