3D Ion Research Articles

Proteomic analysis of plasma membrane and secretory vesicles from human neutrophils

BackgroundPolymorphonuclear neutrophils (PMN) constitute an essential cellular component of innate host defense against microbial invasion and exhibit a wide array of responses both to particulate and soluble stimuli. As the cells recruited earliest during acute inflammation, PMN respond rapidly and release a variety of potent cytotoxic agents within minutes of exposure to microbes or their products. PMN rely on the redistribution of functionally important proteins, from intracellular compartments to the plasma membrane and phagosome, as the means by which to respond quickly. To determine the range of membrane proteins available for rapid recruitment during PMN activation, we analyzed the proteins in subcellular fractions enriched for plasma membrane and secretory vesicles recovered from the light membrane fraction of resting PMN after Percoll gradient centrifugation and free-flow electrophoresis purification using mass spectrometry-based proteomics methods.ResultsTo identify the proteins light membrane fractions enriched for plasma membrane vesicles and secretory vesicles, we employed a proteomic approach, first using MALDI-TOF (peptide mass fingerprinting) and then by HPLC-MS/MS using a 3D ion trap mass spectrometer to analyze the two vesicle populations from resting PMN. We identified several proteins that are functionally important but had not previously been recovered in PMN secretory vesicles. Two such proteins, 5-lipoxygenase-activating protein (FLAP) and dysferlin were further validated by immunoblot analysis.ConclusionOur data demonstrate the broad array of proteins present in secretory vesicles that provides the PMN with the capacity for remarkable and rapid reorganization of its plasma membrane after exposure to proinflammatory agents or stimuli.

Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision‐induced dissociation by malondialdehyde modification of arginine residues

Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.

Spin state transformations of a 3d ion in the pyramidal environment and under latticedistortions

Spin state (SS) transitions in metal-containing pyramidal complexesthat originate from crystallographic distortions are the research subjectof this work. The transition elements are considered to be in the3d6 configuration(Fe2+,Co3+), and they display three different SSs: low-spin(LS,S = 0),intermediate-spin (IS,S = 1) and high-spin (HS,S = 2) states. They have been studied in the frame of the crystal field approximation via the effective nuclearcharge Zeff and under oxygen cage distortions. The features of the SS stability have been calculatedwith/without accounting for spin–orbit coupling. Some critical points at which an accidentaldegeneracy of the SSs exist have been revealed. Near the critical points, negligible distortionscan crucially change the SS. It is demonstrated that the ground SS of the pyramidalMeO5 complex is very sensitive to the symmetry and magnitude of its distortions. SS diagrams in theparameter space ‘effective charge’–‘distortion magnitude’ have been established. It is revealed thatthe IS state exists as a ground state for all considered distortions with a corresponding choice ofZeff. Jahn–Teller distortions stabilize the IS state in a wide range ofZeff. The orbital-like reorientation of the electron density distribution was observed for the ISstate at some threshold magnitude of Jahn–Teller distortions.

Electrospray ionization of uranyl-citrate complexes: Adduct formation and ion-molecule reactions in 3D ion trap and ion cyclotron resonance trapping instruments

Results presented here demonstrate the usefulness of electrospray ionization and gas-phase ion-molecule reactions to predict structural and electronic differences in complex inorganic ions. Electrospray ionization of uranyl citrate solutions generates positively and negatively charged ions that participate in further ion-molecule reactions in 3D ion trap and FT-ICR mass analyzers. Most ions observed are derived from the major solution uranyl-citrate complexes and involve species of {(UO 2) 2Cit 2} 2−, (UO 2) 3Cit 2, and {(UO 2) 3Cit 3} 3−, where Cit indicates the citrate trianion, C 6H 5O 7 3−. In a 3D ion trap operated at relatively high pressure, complex adducts containing solvent molecules, alkali and ammonium cations, and nitrate or chloride anions are dominant, and proton/alkali cation (Na +, K +) exchange is observed for up to six exchangeable protons in an excess of alkali cations. Adduct formation in a FT-ICR cell that is operated at lower pressures is less dominant, and direct detection of positive and negative ions of the major solution complexes is possible. Multiply charged ions are also detected, suggesting the presence of uranium in different oxidation states. Changes in uranium oxidation state are detected by He-CID and SORI-CID fragmentation, and certain fragments undergo association reactions in trapping analyzers, forming “exotic” species such as [(UO 2) 4O 3] −, [(UO 2) 4O 4] −, and [(UO 2) 4O 5] −. Ion-molecule reactions with D 2O in the FT-ICR cell indicate substantial differences in H/D exchange rate and D 2O accommodation for different ion structures and charge states. Most notably, the positively charged ions [H 2(UO 2) 2Cit 2(H)] + and [(UO 2) 2(Cit)] + accommodate two and three D 2O molecules, respectively, which reflects well the structural differences, i.e., tighter uranyl-citrate coordination in the former ion than in the latter. The corresponding negatively charged ions accommodate zero or two D 2O molecules, which can be rationalized using suggested solution phase structures and charge state distributions.

Liquid chromatography/electrospray ionization mass spectrometric characterization of Harpagophytum in equine urine and plasma

A method has been developed for the analysis and characterization in equine urine and plasma of iridoid glycosides: harpagide, harpagoside and 8-para-coumaroyl harpagide, which are the main active principles of Harpagophytum, a plant with antiinflammatory properties. The method involves liquid chromatography coupled with positive electrospray ionization mass spectrometry. The addition of sodium or lithium chloride instead of formic acid in the eluting solvent has been studied in order to enhance the signal and to modify the ion's internal energy. Fragmentation pathways and associated patterns are proposed for each analyte. A comparison of three types of mass spectrometer: a 3D ion trap, a triple quadrupole and a linear ion trap, has been conducted. The 3D ion trap was selected for drug screening analysis whereas the linear ion trap was retained for identification and quantitation analysis.

RT‐PSM, a real‐time program for peptide‐spectrum matching with statistical significance

The analysis of complex biological peptide mixtures by tandem mass spectrometry (MS/MS) produces a huge body of collision-induced dissociation (CID) MS/MS spectra. Several methods have been developed for identifying peptide-spectrum matches (PSMs) by assigning MS/MS spectra to peptides in a database. However, most of these methods either do not give the statistical significance of PSMs (e.g., SEQUEST) or employ time-consuming computational methods to estimate the statistical significance (e.g., PeptideProphet). In this paper, we describe a new algorithm, RT-PSM, which can be used to identify PSMs and estimate their accuracy statistically in real time. RT-PSM first computes PSM scores between an MS/MS spectrum and a set of candidate peptides whose masses are within a preset tolerance of the MS/MS precursor ion mass. Then the computed PSM scores of all candidate peptides are employed to fit the expectation value distribution of the scores into a second-degree polynomial function in PSM score. The statistical significance of the best PSM is estimated by extrapolating the fitting polynomial function to the best PSM score. RT-PSM was tested on two pairs of MS/MS spectrum datasets and protein databases to investigate its performance. The MS/MS spectra were acquired using an ion trap mass spectrometer equipped with a nano-electrospray ionization source. The results show that RT-PSM has good sensitivity and specificity. Using a 55,577-entry protein database and running on a standard Pentium-4, 2.8-GHz CPU personal computer, RT-PSM can process peptide spectra on a sequential, one-by-one basis in 0.047 s on average, compared to more than 7 s per spectrum on average for Sequest and X!Tandem, in their current batch-mode processing implementations. RT-PSM is clearly shown to be fast enough for real-time PSM assignment of MS/MS spectra generated every 3 s or so by a 3D ion trap or by a QqTOF instrument.

Quantitative Comparison of Proteomic Data Quality between a 2D and 3D Quadrupole Ion Trap

A 2D ion trap has a greater ion trapping efficiency, greater ion capacity before observing space-charging effects, and a faster ion ejection rate than a traditional 3D ion trap mass spectrometer. These hardware improvements should result in a significant increase in protein identifications from complex mixtures analyzed using shotgun proteomics. In this study, we compare the quality and quantity of peptide identifications using data-dependent acquisition of tandem mass spectra of peptides between two commercially available ion trap mass spectrometers (an LTQ and an LCQ XP Max). We demonstrate that the increased trapping efficiency, increased ion capacity, and faster ion ejection rate of the LTQ results in greater than 5-fold more protein identifications, better identification of low-abundance proteins, and higher confidence protein identifications when compared with a LCQ XP Max.

The 3D quadrupole ion trap mass spectrometer as a complete chemical laboratory for fundamental gas-phase studies of metal mediated chemistry

Electrospray ionization provides a "treasure trove" of metal containing ions whose fundamental reactivity can be studied via collision induced dissociation and ion-molecule reactions using the multistage mass spectrometry capabilities of the quadrupole ion trap mass spectrometer. Examples of metal mediated chemistry relevant to catalysis, C-C bond coupling, bioinorganic and supramolecular chemistry are highlighted.

Gegenbauer polynomials in a theoretical study of the vibrational structure of the Ca+–H2 system

This work presents an application of Gegenbauer polynomials in vibrational calculations. We illustrated that by example calculations of vibrational structure of the Ca+–H2 exciplex, in the state correlated with 3D calcium ion state. For this case Gegenbauer polynomials are used for formation of a basis set for a bending mode. We showed that this basis set leads to a faster convergence of results than a basis set formed from Legendre polynomials. Additionally we compared vibrational structure obtained in this manner with results of discrete variable representation-distributed Gaussian basis (DVR–DGB) method.

Evolution of the spin state of a 3d ion in a pyramidal complex

The evolution of the spin state of a metallic 3d ion in a pyramidal MeO5 environment is studied. Ions of metals with 3d6 (Fe2+,Co3+) and 3d4 configurations (Mn3+,Cr2+) are studied. The change in the spin state of the metal ion from S=0 to S=1 and S=2 with a variation of the effective charge Zeff of the metal ion and the displacements of the oxygen ions is investigated. The stability of the spin state as a function of the magnitude and symmetry of the displacements of the ligands is checked. Breathing-mode distortions, displacements of the 3d ion along the Z axis, Jahn-Teller distortions of the basal plane of the pyramid, and fluting distortions of the plane of the pyramid are studied. It is shown that different types of distortions produce different behaviors of the terms corresponding to a change in the spin states of all three types. It is found that the spin state of the coordination complex MeO5 with the 3d4 configuration of the metal ion is most sensitive to breathing-mode distortions and Jahn-Teller type distortions stabilize the state with spin S=1 for the 3d6 configuration.

Electron-transfer ion/ion reactions of doubly protonated peptides: effect of elevated bath gas temperature.

In this study, the electron-transfer dissociation (ETD) behavior of cations derived from 27 different peptides (22 of which are tryptic peptides) has been studied in a 3D quadrupole ion trap mass spectrometer. Ion/ion reactions between peptide cations and nitrobenzene anions have been examined at both room temperature and in an elevated temperature bath gas environment to form ETD product ions. From the peptides studied, the ETD sequence coverage tends to be inversely related to peptide size. At room temperature, very high sequence coverage (approximately 100%) was observed for small peptides (< or =7 amino acids). For medium-sized peptides composed of 8-11 amino acids, the average sequence coverage was 46%. Larger peptides with 14 or more amino acids yielded an average sequence coverage of 23%. Elevated-temperature ETD provided increased sequence coverage over room-temperature experiments for the peptides of greater than 7 residues, giving an average of 67% for medium-sized peptides and 63% for larger peptides. Percent ETD, a measure of the extent of electron transfer, has also been calculated for the peptides and also shows an inverse relation with peptide size. Bath gas temperature does not have a consistent effect on percent ETD, however. For the tryptic peptides, fragmentation is localized at the ends of the peptides suggesting that the distribution of charge within the peptide may play an important role in determining fragmentation sites. A triply protonated peptide has also been studied and shows behavior similar to the doubly charged peptides. These preliminary results suggest that for a given charge state there is a maximum size for which high sequence coverage is obtained and that increasing the bath gas temperature can increase this maximum.

Hybrid triple quadrupole‐linear ion trap mass spectrometry in fragmentation mechanism studies: application to structure elucidation of buspirone and one of its metabolites

The use of a hybrid triple quadrupole-linear ion trap (QqQ(LIT)) mass spectrometer system for a comprehensive study of fragmentation mechanisms is described. The anxiolytic drug, buspirone, was chosen as a model compound for this study. With the advent of a QqQ(LIT) instrument, both the traditional quadrupole and the new linear ion trap scans (LIT) could be performed in a single LC run. In the past, a sample had to be run on two different instruments, namely, a triple quadrupole instrument (QqQ) and a 3D ion trap (3D IT) to obtain similar information. With the new QqQ(LIT) technology, collision-induced dissociation (CID) occur in a quadrupole collision cell, q2, and fragment ions are trapped and analyzed in Q3 operated in LIT mode. In this work, high-sensitivity product ion spectra of buspirone were obtained from the one-stage 'Enhanced Product Ion' scan (EPI) with rich product ions and no low mass cut-off. Furthermore, detailed fragmentation pathways were elucidated by further dissociation of each of the fragment ions in the EPI spectrum using MS(3) mode in the same run. The MS(3) scan was performed by incorporating CID in q2, and trapping, cooling, isolation, and resonance-excitation in Q3 when operating in LIT mode. This approach allowed unambiguous assignment of all fragment ions quickly with fewer experiments and easier interpretation than the previous approach. The overall sensitivity for obtaining complete fragment ion data was significantly improved for QqQ(LIT) as compared with that of QqQ and 3D IT mass spectrometers. This is beneficial for structure determination of unknown trace components. The method allowed structure determination of metabolites of buspirone in rat microsomes at 1 microM concentration, which was a 10-fold lower concentration than was needed for QqQ or 3D IT instruments. The QqQ(LIT) instrument provided a simple, rapid, sensitive and powerful approach for structure elucidation of trace components.

Three-dimensional laser-induced fluorescence measurements in a helicon plasma

We describe a three-dimensional (3D) laser-induced fluorescence (LIF) diagnostic for argon ions in a helicon plasma source. With three different laser injection orientations at a single spatial location, LIF measurements are performed to determine the 3D ion temperature and the 3D ion flow vector. The measurement process is then repeated at multiple locations in a cross section of the plasma column to create a two-dimensional (2D) map of the 3D ion flow, the ion temperature, and metastable ion density. Scanning in the 2D plane is accomplished by mounting the injection and collection optics on stepping motor driven stages.

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.

MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS(2)) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS(3). Here, we report that efficient ion capture in a linear ion trap leads to MS(3) acquisition times and spectra quality similar to those for MS(2) experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS(3) spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS(3) spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS(3) spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS(3) spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS(3) identification score can be combined with the MS(2) scores of the precursor peptide from existing search engines. When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.

3-Dimensional Ion Transport in Liquid Crystals

One-dimensional ion transport has been studied in the past decade because of the importance of image retention and voltage holding ratio. Ions inside a liquid crystal (LC) disturb the expected optical behavior of LC molecules when the applied voltage is higher than the LC threshold. In LC devices with complex electrode patterns, interesting ionic effects occur. Advanced and reliable simulation programs are a necessary to investigate this. This paper describes the theory and results of a Monte Carlo 3D ion transport simulation program for LC devices.

Selective Detection of Glycopeptides on Ion Trap Mass Spectrometers

Generation of carbohydrate-specific marker ions during LC-ESMS of digested glycoproteins has been demonstrated to be a highly selective and sensitive approach for detection of glycopeptides. In principle, any mass spectrometer can produce and selectively detect carbohydrate marker ions provided that the instrument is capable of collisional excitation in the region prior to the first mass analyzer sufficient to form abundant oxonium ions. This approach has yet to be demonstrated on 3D ion trap mass spectrometers, which have become widely used for proteomic applications. Here we report the successful development and optimization of carbohydrate marker ion detection on a LCQ Deca 3D ion trap utilizing this scan function. Human alpha-1 acid glycoprotein and a therapeutic monoclonal antibody were chosen to illustrate this methodology. Marker ion detection during LC-ESMS facilitated collection of glycopeptide-containing fractions. Analysis of the glycopeptides in these fractions by MS identified the specific glycosylation sites and enabled the prediction of the family of glycoforms at each attachment site. Using these optimized conditions, marker ion detection and glycopeptide analysis could be achieved with as little as 10 pmol of a glycoprotein.

SIMION modeling of ion optical effects in Cameca ion microanalyzers: simulation of ion transmission losses

A 3D ion optical simulation of the Cameca IMS 3f/4f has been built using the SIMION modeling program and has been combined with a Monte Carlo method to generate initial secondary ion energy and angular distributions. The potential of this modeling system has been demonstrated by evaluating ion transmission losses in the IMS 3f/4f.

Application of time-sliced ion velocity imaging to crossed molecular beam experiments

A three-dimensional (3D) ion velocity imaging method was developed to measure the product velocity distributions in crossed molecular beam experiments. While maintaining conventional two-dimension velocity mapping, the third velocity component was mapped linearly to the ion time of flight. A weak extraction field was used to spread the ion turnaround time to several hundred nanoseconds, which permits good resolution for selection of the longitudinal velocity. A fast gated (⩾5 ns) intensified charge coupled device camera was used to record time-sliced ion images. Calibration of the apparatus was done by measuring O+ images from the multiphoton dissociation/ionization of O2. The resolution in velocity achieved was about 1% (Δv/v) in slicing through the center of a Newton sphere. The overall performance was examined by observing product ion images from the F+CD4→DF+CD3 reaction. To detect CD3+ with kinetic energy release of about 1 eV, 50 ns time slicing provides sufficient velocity resolution, such that resolution of the image is mainly limited by the spread in velocity of the two molecular beams. These ion optics can focus on a large volume of ion cloud, which is crucial in crossed molecular beam experiments. Direct 3D imaging also simplifies data analysis. This direct 3D ion imaging method provides a powerful tool with which to study systems with no cylindrical symmetry.

Rapid screening and characterization of drug metabolites using a new quadrupole-linear ion trap mass spectrometer.

The application of a new hybrid RF/DC quadrupole-linear ion trap mass spectrometer to support drug metabolism and pharmacokinetic studies is described. The instrument is based on a quadrupole ion path and is capable of conventional tandem mass spectrometry (MS/MS) as well as several high-sensitivity ion trap MS scans using the final quadrupole as a linear ion trap. Several pharmaceutical compounds, including trocade, remikiren and tolcapone, were used to evaluate the capabilities of the system with positive and negative turbo ionspray, using either information-dependent data acquisition (IDA) or targeted analysis for the screening, identification and quantification of metabolites. Owing to the MS/MS in-space configuration, quadrupole-like CID spectra with ion trap sensitivity can be obtained without the classical low mass cutoff of 3D ion traps. The system also has MS(3) capability which allows fragmentation cascades to be followed. The combination of constant neutral loss or precursor ion scan with the enhanced product ion scan was found to be very selective for identifying metabolites at the picogram level in very complex matrices. Owing to the very high cycle time and, depending on the mass range, up to eight different MS experiments could be performed simultaneously without compromising chromatographic performance. Targeted product ion analysis was found to be complementary to IDA, in particular for very low concentrations. Comparable sensitivity was found in enhanced product ion scan and selected reaction monitoring modes. The instrument is particularly suitable for both qualitative and quantitative analysis.

Syntheses, X-ray crystal structures, and magnetic properties of novel linear M2[II]U[IV] complexes (M=Co, Ni, Cu, Zn).

Attempts to prepare heterobimetallic complexes in which 3d and uranium magnetic ions are associated by means of the Schiff bases H(2)L(i) derived from 2-hydroxybenzaldehyde or 2-hydroxy-3-methoxybenzaldehyde were unsuccessful because of ligand transfer reactions between [ML(i)] (M=Co, Ni, Cu) and UCl(4) that led to the mononuclear Schiff base complexes of uranium [UL(i)Cl(2)]. The crystal structure of [UL(3)Cl(2)(py)(2)] [L(3)=N,N'-bis(3-methoxysalicylidene)-ethylenediamine; py=pyridine] was determined. The hexadentate Schiff base ligand N,N'-bis(3-hydroxysalicylidene)-2,2-dimethyl-1,3-propanediamine (L) was useful for the synthesis of novel trinuclear complexes of the general formula [[ML(py)](2)U] (M=Co, Ni, Zn) or [[CuL(py)]M'[CuL]] (M'=U, Th, Zr) by reaction of [M(H(2)L)] with [M'(acac)(4)] (acac=MeCOCHCOMe). The crystal structures of the Co(2)U, Ni(2)U, Zn(2)U, Cu(2)U, and Cu(2)Th complexes show that the two ML fragments are orthogonal, being linked to the central actinide ion by the two pairs of oxygen atoms of the Schiff base ligand. In each compound, the UO(8) core exhibits the same dodecahedral geometry, and the three metals are linear. The magnetic study indicated that the two Cu(2+) ions are not coupled in the Cu(2)Zr and Cu(2)Th compounds. The magnetic behavior of the Co(2)U, Ni(2)U, and Cu(2)U complexes was compared with that of the Zn(2)U derivative, in which the paramagnetic 3d ion was replaced with the diamagnetic Zn(2+) ion. A weak antiferromagnetic coupling was observed between the Ni(2+) and the U(4+) ions, while a ferromagnetic interaction was revealed between the Cu(2+) and U(4+) ions.