The effect of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry instrumentation parameters on the matrix-assisted laser desorption/ionization simulated size exclusion chromatography number-mass, average-weight and polydispersity values of dextran against corresponding values obtained by size exclusion chromatography

The matrix-assisted laser desorption/ionization simulated size exclusion chromatography (SECPC) average-number mass, weight average and polydispersity of dextran 1000 were determined by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. The instrument parameters were varied and the SECPC value determined via the Bruker XMASS software was compared to the value obtained from aqueous-phase size exclusion chromatography. The aqueous-phase size exclusion chromatography values for average-number mass, weight average and polydispersity were 1223 Da, 1500 Da and 1.23 (1010 Da, 1270 Da and 1.26 from manufacturer), whereas the SECPC value varied on the instrumental parameters. The factors that had the greatest effect on the average-number mass, weight average and polydispersity were: (most effect on SECPC value) laser attenuation > matrix-analyte molar concentration > matrix-analyte molar ratios > delay extraction time > solvent-system composition > detector delay (least effect on SECPC value). The oligosaccharide signal distribution as a function of laser attenuation indicate that two distinct regions exist in dextran 1000, where one corresponds to the higher mass oligosaccharides (hexasaccharide or greater), while another region corresponds to lower oligosaccharides (tetra-saccharide). This distribution depends upon the crystallization of the biopolymer and the efficiency of desorption/ionization, which yields the SECPC value. There was broad agreement between the SECPC values and size exclusion chromatography values for dextran, although the polydispersity indicated by SECPC was less than size exclusion chromatography (1.10 vs. 1.26). It can be shown that for narrow polydisperse biopolymers the instrumental conditions are less critical in the determination of average-number mass, weight average and polydispersity, although the SECPC Mn, and weight average values are often higher than the corresponding values obtained by aqueous-phase size exclusion chromatography.

Space-charge effects in an electrostatic multireflection ion trap

The multireflection ion traps with isochronous properties offer a Lot of opportunities for time-of-flight mass spectrometry by elongation of the ion path, thus preserving the compact dimensions of an instrument. We have built and tested a two-mirror linear trap that provides at least 80,000 mass-resolving power. Although the mass resolution appears promising, there are substantial limitations that arise from Coulomb interactions of the trapped ions. Among these, the mutual repulsion of ions with same or close mass-to-charge ratios appears dominant, resulting in counterintuitive motion synchronization. The self-bunching and coalescence effects are also examined by numerical simulation.

Determination of end groups of synthetic polymers by matrix-assisted laser desorption/ionization: high-energy collision-induced dissociation

Matrix-assisted laser desorption/ionization has been combined with high-energy collision-induced dissociation for the analysis of poly(ethylene glycols) with butanoyl, benzoyl and acetyl end groups, using novel technology comprising a magnetic-sector mass spectrometer and ion buncher with an in-line quadratic-field ion mirror. High-energy (>8 keV) collision-induced dissociation facilitated unambiguous end-group determination of these polymers, providing masses of end groups and structural information. The high-energy collision-induced dissociation also provided information regarding repeat units.

High-energy collision induced dissociation fragmentation pathways of peptides, probed using a multiturn tandem time-of-flight mass spectrometer "MULTUM-TOF/TOF"

A new multiturn tandem time-of-flight (TOF) mass spectrometer "MULTUM-TOF/TOF" has been designed and constructed. It consists of a matrix-assisted laser desorption/ionization ion source, a multiturn TOF mass spectrometer, a collision cell, and a quadratic-field ion mirror. The multiturn TOF mass spectrometer can overcome the problem of precursor ion selection in TOF, due to insufficient time separation between two adjacent TOF peaks, by increasing the number of cycles. As a result, the total TOF increases with the increase in resolving power. The quadratic-field ion mirror allows temporal focusing for fragment ions with different kinetic energies. Product ion spectra from monoisotopically selected precursor ions of angiotensin I, substance P, and bradykinin have been obtained. The fragment ions observed are mainly the result of high-energy collision induced dissociation.

Chemical cross-linking and mass spectrometry as structure determination tools

Chemical cross-linking is becoming a valuable tool for the high-order structure determination of proteins and protein complexes. Cross-linking methodology is able to provide low-resolution structures when at least something is known already about the proteins under investigation. The suitability of top-down and bottom-up methodologies is discussed and further potential applications of chemical cross-linking of proteins, as well as combinations with other techniques such as hydrogen/deuterium exchange and molecular modeling, are suggested.

Monitoring conformational changes in protein complexes using chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: the effect of calcium binding on the calmodulin-melittin complex

Calmodulin is an EF hand calcium binding protein. Its binding affinities to various protein/peptide targets often depend on the conformational changes induced by the binding of calcium. One such target is melittin, which binds tightly to calmodulin in the presence of calcium, and inhibits its function. Chemical cross-linking combined with Fourier transform ion cyclotron resonance mass spectrometry has been employed to investigate the coordination of calmodulin and melittin in the complex at different concentrations of calcium. This methodology can be used to monitor structural changes of proteins induced by ligand binding, and study the effects these changes have on non- covalent interactions between proteins. Cross-linking results indicate that the binding place of the first melittin in the calcium free calmodulin form is the same as in the calcium loaded calmodulin/melittin complex.

A tandem time-of-flight mass spectrometer: combination of a multi-turn time-of-flight and a quadratic-field mirror

A tandem time-of-flight (ToF) mass spectrometer consisting of a multi-turn time-of-flight (ToF) and a quadratic-field ion mirror has been designed and constructed. The instrument combines the unique capabilities of both ToF instruments, namely high-resolution and monoisotopic precursor ion selection from the multi-turn ToF and temporal focus for fragment ions with different kinetic energies from the quadratic-field mirror. The first tandem mass spectra for this unique combination of ToF systems are presented.

Identification of a Cluster of Genes that Directs Desferrioxamine Biosynthesis in Streptomyces coelicolor M145

Desferrioxamines are a structurally related family of tris-hydroxamate siderophores that form strong hexadentate complexes with ferric iron. Desferrioxamine B has been used clinically for the treatment of iron overload in man. We have unambiguously identified desferrioxamine E as the major desferrioxamine siderophore produced by Streptomyces coelicolor M145 and have identified a cluster of four genes (desA-D) that directs desferrioxamine biosynthesis in this model actinomycete. On the basis of comparative sequence analysis of the proteins encoded by these genes, we propose a plausible pathway for desferrioxamine biosynthesis. The desferrioxamine biosynthetic pathway belongs to a new and rapidly emerging family of pathways for siderophore biosynthesis, widely distributed across diverse species of bacteria, which is biochemically distinct from the better known nonribosomal peptide synthetase (NRPS) pathway used in many organisms for siderophore biosynthesis.

Production and Properties of Nanoelectrospray Emitters Used in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Implications for Determination of Association Constants for Noncovalent Complexes

Electrospray ionization (ESI) is extensively used in the analysis of biological compounds; yet some fundamental properties of this technique are not completely understood. It is widely recognized that care should be exercised when noncovalent complexes are being studied by ESI, since weak noncovalent binding can be broken or formed during the desolvation process. In the present work, spectra from the noncovalent complex, vancomycin/diacetyl-L-lysyl-D-alanyl-D-alanine, obtained from ESI and from nanoelectrospray ionization (nanoESI), have been compared. The results indicated that the milder desolvation conditions arising as a result of the smaller sizes of droplets produced in the nanoESI source attenuated effects upon weak bonds in the desolvation process. The association constant values calculated from the relative peak intensities suggest that, when using ESI, the analyzed noncovalent complex dissociated in the condensed phase during the spraying process. The influences of experimental parameters such as tip diameter and coating for nanoESI needles were investigated. Principal component analysis, a multivariate analysis method, was applied to achieve a better evaluation of the spectra obtained using different needle diameters and coatings for the analysis of the noncovalent complex vancomycin/diacetyl-L-lysyl-D-alanyl-D-alanine. It was found that 2-microm tip diameter resulted in more reproducible spectra than the larger tip diameters tested (6-20 microm).

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay

In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.

The Ion Conveyor. An ion focusing and conveying device

The control and transmission of ions or small charged droplets in the intermediate to high-pressure regime is of primary importance in areas such as atmospheric pressure ionisation. Where small apertures separate differentially pumped vacuum regions in the inlet systems to mass spectrometers, a large proportion of the available ion current is lost to the surrounding electrode structures. A new ion-optical device, named the ion conveyor, incorporating electrodynamic focusing and conveying of charged entities is described. Results from ion-optical simulations are presented demonstrating the performance of the device in various operating modes and electrode configurations.

Discrimination Effects in MALDI-MS of Mixtures of Peptides—Analysis of the Proteome

Peptide ion suppression in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) can hinder the detection of site-specific post-translational protein modifications. Within a peptide mixture, the presence or absence of a particular peptide can affect the ion intensities of other peptides in the mixture. These effects have been studied using equimolar solutions of target peptides and observation of the increase or decrease in ion intensity of the peptides upon the removal or addition of individual peptides. Gas-phase basicities and hydrophobicity measures have been used to rationalize this behaviour. ZipTips have been used to remove impurities and reduce the number of peptides present at any moment in a solution, a procedure that results in a significant increase in the total percentage of the amino acid coverage of enzymatically digested proteins. The efficacy of this approach was demonstrated using specifically nitrated lysozyme and specifically nitrated myoglobin.

Profiling of cyclic hexadepsipeptides roseotoxins synthesized in vitro and in vivo: a combined tandem mass spectrometry and quantum chemical study

High-performance liquid chromatography and tandem mass spectrometry (HPLC/MS/MS) was used for the detection of cyclic hexadepsipeptides roseotoxins produced by Trichothecium roseum. Roseotoxins were found in both submerged standard cultivation on CzapekDox medium and in vivo cultivation extract obtained from an apple. Roseotoxin chromatographic profiles from these two experiments were compared. Product-ion collision-induced dissociation (CID) spectra obtained on an ion trap (electrospray ionisation, ESI) were used for the identification of natural roseotoxins A, B, C and of minor destruxins A and B. The dissociation behavior of roseotoxins is discussed in terms of a fragmentation scheme proposed for describing the dissociation pathways of cyclic peptides. This scheme involves opening of the cyclopeptide ring via formation of oxazolone derivatives and fragmentation of the resulting linear species, which have a free N-terminus and an oxazolone ring at the C-terminus. Some aspects of this fragmentation scheme are underlined by modeling the dissociation channels of roseotoxin A using quantum chemical calculations. The structures of roseotoxin A and destruxin B were verified by nuclear magnetic resonance (NMR) spectroscopy. Structures of three new minor natural roseotoxins [Val(4)]RosA, [MeLxx(4)]RosA and [MeLxx(4)]RosB were deduced by ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT-MS) and ion trap tandem mass spectrometry by examining the pre-separated roseotoxin fraction.