Ion soft landing using a rectilinear ion trap mass spectrometer

A new ion soft landing instrument has been built for the controlled deposition of mass selected polyatomic ions. The instrument has been operated with an electrospray ionization source; its major components are an electrodynamic ion funnel to reduce ion loss, a 90-degree bent square quadrupole that prevents deposition of fast neutral molecules onto the landing surface, and a novel rectilinear ion trap (RIT) mass analyzer. The ion trap is elongated (inner dimensions: 8 mm x 10 mm x 10 cm). Three methods of mass analysis have been implemented. (i) A conventional mass-selective instability scan with radial resonance ejection can provide a complete mass spectrum. (ii) The RIT can also be operated as a continuous rf/dc mass filter for isolation and subsequent soft landing of ions of the desired m/ z value. (iii) The 90-degree bent square quadrupole can also be used as a continuous rf/dc mass filter. The mass resolution (50% definition) of the RIT in the trapping mode (radial ion ejection) is approximately 550. Ions from various test mixtures have been mass selected and collected on fluorinated self-assembled monolayers on gold substrates, as verified by analysis of the surface rinses. Desorption electrospray ionization (DESI) has been used to confirm intact deposition of [Val (5)]-Angiotensin I on a surface. Nonmass selective currents up to 1.1 nA and mass-selected currents of up to 500 pA have been collected at the landing surface using continuous rf/dc filtering with the RIT. A quantitative analysis of rinsed surfaces showed that the overall solution-to-solution soft landing yields are between 0.2 and 0.4%. Similar experiments were performed with rf/dc isolation of both arginine and lysine from a mixture using the bent square quadrupole in the rf/dc mode. The unconventional continuous mass selection methods maximize soft landing yields, while still allowing the simple acquisition of full mass spectra.     

Preparative linear ion trap mass spectrometer for separation and collection of purified proteins and peptides in arrays using ion soft landing

A preparative mass spectrometer for microarray fabrication is reported. The instrument includes an atmospheric pressure ionization source, a linear ion trap mass analyzer, an ion collection surface positioning system, and a surface loading chamber with independent vacuum pumping. It was designed for the production of protein arrays using the ion soft-landing technique to collect ions on a surface after separation by mass/charge ratio. Small microarrays have been prepared by isolating and soft landing individual protein or peptide ions after electrospray ionization of mixtures. The composition and purity of the separated materials has been confirmed using independent external mass spectrometric analysis of rinse solutions of the collected spots, either by the new method of electrosonic spray ionization MS or by nanospray ionization MS. The ability to retain bioactivity in the mass-selected and collected biomolecules has been demonstrated in particular cases. The reported instrument has also been characterized as an analytical mass spectrometer.     

Ambient ion soft landing

Ambient ion soft landing, a process in which polyatomic ions are deposited from air onto a surface at a specified location under atmospheric pressure, is described. Ions generated by electrospray ionization are passed pneumatically through a heated metal drying tube, their ion polarity is selected using ion deflectors, and the dry selected ions are soft-landed onto a selected surface. Unlike the corresponding vacuum soft-landing experiment, where ions are mass-selected and soft-landed within a mass spectrometer, here the ions to be deposited are selected through the choice of a compound that gives predominantly one ionic species upon ambient ionization; no mass analysis is performed during the soft landing experiment. The desired dry ions, after electrical separation from neutrals and counterions, are deposited on a surface. Characterization of the landed material was achieved by dissolution and analysis using mass spectrometry or spectrofluorimetry. The treated surface was also characterized using fluorescence microscopy, which allowed surfaces patterned with fluorescent compounds to be imaged. The pure dry ions were used as reagents in heterogeneous ion/surface reactions including the reaction of pyrylium cations with d-lysine to form the N-substituted pyridinium cation. The charged microdroplets associated with incompletely dried ions could be selected for soft landing or surface reaction by choice of the temperature of a drying tube inserted between the ion source and the electrical ion deflectors.     

Electrospray ion beam deposition of clusters and biomolecules

An ion beam source using electrospray ionization is presented for nondestructive vacuum deposition of mass-selected large organic molecules and inorganic clusters. Electrospray ionization is used to create an ion beam from a solution containing the nanoparticles or molecules to be deposited. To form and guide the ion beam, radio frequency and electrostatic ion optics are utilized. The kinetic energy distribution of the particles is measured to control the beam formation and the landing process. The particle mass-to-charge ratio is analyzed by in situ time-of-flight mass spectrometry. To demonstrate the performance of the setup, deposition experiments with gold nanoclusters and bovine serum albumin proteins on graphite surfaces were performed and analyzed by ex situ atomic force microscopy. The small gold clusters are found to form three-dimensional agglomerations at the surface, preferentially decorating the step edges. In contrast, bovine serum albumin creates two-dimensional fractal nanostructures on the substrate terraces due to strong intermolecular interactions.     

Preparation and in situ characterization of surfaces using soft landing in a Fourier transform ion cyclotron resonance mass spectrometer

Mass-selected peptide ions produced by electrospray ionization were deposited onto fluorinated self-assembled monolayer surfaces (FSAM) surfaces by soft landing using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially designed for studying interactions of large ions with surfaces. Analysis of the modified surface was performed in situ by combining 2-keV Cs+ secondary ion mass spectrometry with FT-ICR detection of the sputtered ions (FT-ICR-SIMS). Regardless of the initial charge state of the precursor ion, the SIMS mass spectra included singly protonated peptide ion, peptide fragment ions, and peaks characteristic of the surface in all cases. In some experiments, multiply protonated peptide ions and [M + Au]+ ions were also observed upon SIMS analysis of modified surfaces. For comparison with the in situ analysis of the modified surfaces, ex situ analysis of some of the modified surfaces was performed by 25-keV Ga+ time-of-flight-secondary ion mass spectrometry (TOF-SIMS). The ex situ analysis demonstrated that a significant number of soft-landed peptide ions remain charged on the surface even when exposed to air for several hours after deposition. Charge retention of soft-landed ions dramatically increases the ion yields obtained during SIMS analysis and enables very sensitive detection of deposited material at less than 1% of monolayer coverage. Accumulation of charged species on the surface undergoes saturation due to coulomb repulsion between charges at close to 30% coverage. We estimated that close to 1 ng of peptide could be deposited on the spot area of 4 mm2 of the FSAM surface without reaching saturation.     

Preparative soft and reactive landing of gas-phase ions on plasma-treated metal surfaces

Soft landing of singly charged gas-phase ions on dry metal surfaces that were pretreated in situ by oxygen plasma results in 0.1-2% total yields of recovered intact compounds. Lysine, peptides, crystal violet dye, and a biotin conjugate are found to survive soft landing of hyperthermal ions of up to 50-eV kinetic energy. Soft landing at 40-50-eV ion kinetic energies of a fluorescence-labeled biotin conjugate results in an immobilized fraction that cannot be washed from the surface and is found to contain an intact biotin moiety. The present results represent an approximately 10(4) fold improvement in soft-landing efficiency and indicate that plasma-treated metal surfaces can be useful for preparative separation of organic and biological molecules by mass spectrometry. The substantial improvement in soft-landing yields results from a high transmission of electrosprayed ions into the vacuum system, efficient and nondestructive discharge of ions on the metal oxide surface, and facile analyte recovery in the absence of a matrix.     

Positive ion transmission mode ion/ion reactions in a hybrid linear ion trap

A triple quadrupole mass spectrometer capable of ion trapping experiments has been adapted for ion/ion reaction studies. The instrument is based on a commercially available linear ion trap (LIT) tandem mass spectrometer (i.e., an MDS SCIEX 2000 Q TRAP) that has been modified by mounting an atmospheric sampling glow discharge ionization (ASGDI) source to the side of the vacuum manifold for production of singly charged anions. The ASGDI source is located line of sight to the side of the third quadrupole of the triple quadrupole assembly (Q3). Anions are focused into the side of the rod array (i.e., anion injection occurs orthogonal to the normal ion flight path). A transmission mode method to perform ion/ion reactions has been developed whereby positive ions are transmitted through the pressurized collision quadrupole (Q2) while anions are stored in Q2. The Q2 LIT is used to trap negative ions whereas the Q3 LIT is used to accumulate positive ions transmitted from Q2. Anions are injected to Q3 and transferred to Q2, where they are stored and collisionally cooled. Multiply charged protein/peptide ions, formed by electrospray, are then mass selected by the first quadrupole assembly (Q1) operated in the rf/dc mode and injected into Q2. The positive ions, including the residual precursor ions and the product ions arising from ion/ion proton-transfer reactions, are accumulated in Q3 until they are analyzed via mass-selective axial ejection for mass analysis. The parameters that affect ion/ion reactions are discussed, including pressure, nature of the gas in Q2, and operation of Q2 as a linear accelerator. Ion/ion reactions in this mode can be readily utilized to separate ions with the same m/z but largely different mass and charge, e.g., +1 bradykinin and +16 myoglobin, in the gas phase.     

A tandem ion trap/ion mobility spectrometer

A tandem quadrupole ion trap/ion mobility spectrometer (QIT/IMS) has been constructed for structural analysis based on the gas-phase mobilities of mass-selected ions. The instrument combines the ion accumulation, manipulation, and mass-selection capabilities of a modified ion trap mass spectrometer with gas-phase electrophoretic separation in a custom-built ion mobility drift cell. The quadrupole ion trap may be operated as a conventional mass spectrometer, with ion detection using an off-axis dynode/multiplier arrangement, or as an ion source for the IMS drift cell. In the latter case, pulses of ions are ejected from the trap and transferred to the drift cell where mobility in the presence of helium buffer gas is determined by the collision cross section of the ion. Ions traversing the drift cell are detected by an in-line electron multiplier and the data processed with a multichannel scaler. Preliminary data are presented on instrumental performance characteristics and the application of QIT/ IMS to structural and conformational studies of aromatic ions and protonated amine/crown ether noncovalent complexes generated via ion/molecule reactions in the ion trap.     

Surface modification using a commercial triple quadrupole mass spectrometer

We report instrumental modifications to a commercial mass spectrometer that allow surface modification experiments to be performed using low-energy (electronvolt range) mass-selected ion beams. The design of the detector housing allows placement of the surface on the ion optical axis and some distance beyond the off-axis detector. Manipulation of the potentials applied to the final lens, detector housing, conversion dynode, and electron multiplier allow the ions to pass through the detector housing and impinge upon the surface without loss of the normal mode of detector operation. Ex situ analysis of the modified surface is performed using a home-built multisector mass spectrometer. The ability to modify organic thin films is demonstrated by a number of soft landing and surface modification experiments including (i) soft landing of (CH3)2SiNCS+ ions formed from trimethylsilyl isothiocyanate upon a fluorinated self-assembled monolayer (F-SAM) surface, (ii) soft landing and dissociative soft landing of the pseudomolecular cation of triphenylpyrylium tetrafluoroborate, viz. the triphenylpyrylium cation, upon an F-SAM surface, (iii) dissociative soft landing of 35ClCH2(CH3)2SiOSi(CH3)2+ formed from 1,3-bis(chloromethyl)disiloxane upon an F-SAM surface, (iv) surface passivation by reaction of the trimethylsilyl cation, Si(CH3)3+, with a hydroxyl-terminated self-assembled monolayer (OH-SAM), and (v) transhalogenation by reaction of CCl3+ (m/z 119) with an F-SAM surface.     

Preparative separation of mixtures by mass spectrometry

A specially designed mass spectrometer which allows for preparative separation of mixtures is described. This mass spectrometer allows for large ion currents, on the order of nanoamperes, to be produced by electrospray and transmitted into a high vacuum. Accumulation of nanomole quantities of collected and recovered material in several hours is demonstrated. The use of high-velocity ions reduces space charge effects at high ion currents. Separation of mass occurs simultaneously for all ions, providing a 100% duty cycle. The use of a linear dispersion magnet avoids compression at higher m/z ratios. A deceleration lens slows the ions to allow for soft landing at low kinetic energy. The ions are neutralized by ion pairing on an oxidized metal surface. Retractable landing plates allow for easy removal of the separated components.     

Surface-enhanced Raman spectroscopy of soft-landed polyatomic ions and molecules

Surface-enhanced Raman spectroscopy (SERS) was used to detect and characterize polyatomic cations and molecules that were electrosprayed into the gas phase and soft-landed in vacuum on plasma-treated silver substrates. Organic dyes such as crystal violet and Rhodamine B, the nucleobase cytosine, and nucleosides cytidine and 2'-deoxycytidine were immobilized by soft landing on plasma-treated metal surfaces at kinetic energies ranging from near thermal to 200 eV. While enhancing Raman scattering 10(5)-10(6)-fold, the metal surface effectively quenches the fluorescence that does not interfere with the Raman spectra. SERS spectra from submonolayer amounts of soft-landed compounds were sufficiently intense and reproducible to allow identification of Raman active vibrational modes for structure assignment. Soft-landed species appear to be microsolvated on the surface and bound via ion pairing or pi-complexation to the Ag atoms and ions in the surface oxide layer. Comparison of spectra from soft-landed and solution samples indicates that the molecules survive soft landing without significant chemical damage even when they strike the surface at hyperthermal collision energies.     

Vibrational spectroscopy and mass spectrometry for characterization of soft landed polyatomic molecules

We report implementation of two powerful characterization tools, in situ secondary ion mass spectrometry (SIMS) and ex situ surface enhanced Raman spectroscopy (SERS), in analyzing surfaces modified by ion soft landing (SL). Cations derived from Rhodamine 6G are soft landed onto Raman-active silver colloidal substrates and detected using SERS. Alternatively and more conveniently, high-quality SERS data are obtained by spin coating a silver colloidal solution over the modified surface once SL is complete. Well-defined SERS features are observed for Rhodamine 6G in as little as 15 min of ion deposition. Deposition of ~3 pmo1 gave high-quality SERS spectra with characteristic spectroscopic responses being derived from just ~0.5 fmol of material. Confocal SERS imaging allowed the enhancement to be followed in different parts of deposited dried droplets on surfaces. Characteristic changes in Raman spectral features occur when Rhodamine 6G is deposited under conditions that favor gas-phase ion fragmentation. Simultaneous deposition of both the intact dye and its fragment ion occurs and is confirmed by SIMS analysis. The study was extended to other Raman active surfaces, including Au nanostar and Au coated Ni nanocarpet surfaces and to SL of other molecules including fluorescein and methyl red. Overall, the results suggest that combination of SERS and SIMS measurements are effective in the characterization of surfaces produced by ion SL with significantly enhanced molecular specificity.     

Tandem time-of-flight mass spectrometry with a curved field reflectron

The unique focusing properties of the curved-field reflectron provide a simple solution to the problem of compensating for the broad range of energies of product ions produced postsource in a time-of-flight mass spectrometer. This has been shown previously for the technique known as postsource decay, but in this report we demonstrate its use for tandem time-of-flight mass spectrometry using a high-performance MALDI time-of-flight instrument modified by the addition of a collision chamber to enable the recording of mass-selected product ions formed by collision-induced dissociation (CID). In particular, the curved-field reflectron enables the use of the full 20-keV kinetic energy provided by the ion source extraction voltage as the collision energy in the laboratory frame and obviates the need to reaccelerate the product ions, using a second "source" or "lift" cell. Results are presented for the collision-induced dissociation of fullerenes over a range of collision gas pressures and precursor ion attenuation. In addition, CID tandem mass spectra are obtained for several peptides.     

激光-分子束-表面散射装置的研制

介绍了自行设计和加工的激光-分子束-表面散射装置，并对超高真空转动密封结构作了详细描述。差分泵浦的超音速分子束对准样品中心，射入超高真空主室。样品架安放在主室中央，四极质谱检测器可绕样品转动，用来测量表面散射分子的平动能及角分布。三个石英窗口作为激光窗口，可用LIF或MPI方法来测量表面散射分子的内能态分布，也可用于研究表面光化学。最后给出了分子束发散角及室温时CH2I2在Ag（110）表面用308um激光光解碎片碘的TOF谱的测量结果。     

Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer

A commercial quadrupole/time-of-flight (QqTOF) tandem mass spectrometer has been adapted for ion/ion reaction studies. To enable mutual storage of oppositely charged ions in a linear ion trap, the oscillating quadrupole field of the second quadrupole of the system (Q2) serves to store ions in the radial dimension while auxiliary radio frequency is superposed on the end lenses of Q2 during the reaction period to create barriers in the axial dimension. A pulsed dual electrospray (ESI) source is directly coupled to the instrument interface for the purpose of proton transfer reactions. Singly and doubly charged protein ions as high in mass as 66 kDa are readily formed and observed after proton-transfer reactions. For the modified instrument, the mass resolving power is approximately 8000 for a wide m/z range, and the mass accuracy is approximately 20 ppm for external calibration and approximately 5 ppm for internal calibration after ion/ion reactions. Parallel ion parking is demonstrated with a six-component protein mixture, which shows the potential application of reducing spectral complexity and concentrating certain charge states. The current system has high flexibility with respect to defining MS(n) experiments involving collision-induced dissociation (CID) and ion/ion reactions. Protein precursor and CID product masses can be determined with good accuracy, providing an attractive platform for top-down proteomics. Electron transfer dissociation ion/ion reactions are implemented by using a pulsed nano-ESI/atmospheric pressure chemical ionization dual source for ionization. The reaction between protonated peptide ions and radical anions of 1,3-dinitrobenzene formed exclusively c- and z-type fragment ions.     

Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis

The design and operation of a novel UV-MALDI ionization source on a commercial QqoaTOF mass spectrometer (Applied Biosystem/MDS Sciex QSTAR Pulsar) is described. Samples are loaded on a 96-well target plate, the movement of which is under software control and can be readily automated. Unlike conventional high-energy MALDI-TOF, the ions are produced with low energies (5-10 eV) in a region of relatively low vacuum (8 mTorr). Thus, they are cooled by extensive low-energy collisions before selection in the quadrupole mass analyzer (Q1), potentially giving a quasi-continuous ion beam ideally suited to the oaTOF used for mass analysis of the fragment ions, although ion yields from individual laser shots may vary widely. Ion dissociation is induced by collisions with argon in an rf-only quadrupole cell, giving typical low-energy CID spectra for protonated peptide ions. Ions separated in the oaTOF are registered by a four-anode detector and time-to-digital converter and accumulated in "bins" that are 625 ps wide. Peak shapes depend upon the number of ion counts in adjacent bins. As expected, the accuracy of mass measurement is shown to be dependent upon the number of ions recorded for a particular peak. With internal calibration, mass accuracy better than 10 ppm is attainable for peaks that contain sufficient ions to give well-defined Gaussian profiles. By virtue of its high resolution, capability for accurate mass measurements, and sensitivity in the low-femotomole range, this instrument is ideally suited to protein identification for proteomic applications by generation of peptide tags, manual sequence interpretation, identification of modifications such as phosphorylation, and protein structural elucidation. Unlike the multiply charged ions typical of electrospray ionization, the singly charged MALDI-generated peptide ions show a linear dependence of optimal collision energy upon molecular mass, which is advantageous for automated operation. It is shown that the novel pulsing technique of this instrument that increases the sensitivity for precursor ions scans is applicable to the identification of peptides labeled with isotope-coded affinity tags.     

Placing and imaging individual carbon nanotubes on Cu(111) clean surface using in situ pulsed-jet deposition-STM technique

We report pulsed-jet deposition of single-wall and double-wall carbon nanotubes (SWNTs and DWNTs; CNTs) onto a clean Cu(111) surface and their scanning tunneling microscopy (STM) observations under ultra-high vacuum (UHV). The clean Cu(111) surface prepared by a repeated Ar-sputtering and annealing is introduced into a load-lock chamber kept at a 10(-5)-Pa range vacuum, and the CNTs dispersed in a chloroform solution by ultrasonication are pulse-injected onto the surface. Since the substrate is annealed at 700 K to remove the residual solvent molecules, high resolution lattice images of the CNTs are successfully observed by STM. High-resolution chirality-resolved images of the two SWNTs with a metal cluster are also observed, supporting the well accepted growth mechanism of the CNTs from the metal-catalyst cluster. The present pulsed-jet deposition in high-vacuum is superior to the conventional spin-coating or drop-coating techniques for preparing clean and well-defined CNTs on clean surfaces for high-resolution and contamination-free UHV-STM observation.     

Ion induced gas desorption problems in the ISR

Not least among the many stringent conditions which must be satisfied to achieve the proper operation of the Intersecting Storage Rings at CERN are those pertaining to its 2 km of ultrahigh vacuum. Apart from the direct influence of the residual gas molecules through nuclear and Coulomb scattering on the stored beam lifetimes (of the order of days during which the stored protons should travel the astronomical distance of some light days!) there are also indirect processes which additionally involve adsorption/desorption phenomena on the vacuum chamber wall. The beam of high energy protons creates low energy secondary ions in the residual gas. These ions, generated in the space charge potential of 1 kV (10 A)^?1 of proton beam, are accelerated by this potential onto the stainless steel vacuum chamber wall where a variety of adsorption/desorption phenomena may be stimulated. Desorbed molecules are fed back into the residual gas resulting in the possibility of creating an unstable run-away pressure increase which can finally destroy the stored beam. This danger depends on the local parameters of the vacuum system, and most critically, on the state of the vacuum chamber surface.The paper summarises recent observations in this field and describes the results of investigations aimed at producing cleaner surfaces in vacuum chambers. These investigations, which have included high temperature bakeouts, ion bombardment scrubbing by glow discharge, oxidation, etc, will show that under favourable conditions, net negative desorption coefficients can be obtained which turn the Intersecting Storage Rings into a large ion pump. Results, supported and compared with measurements using Auger and Sims surface analysis, are presented mainly from the empirical point of view with the emphasis on practical implications for machines where the surfaces of the vacuum system are subjected to ion bombardment.     

A quadrupole ion trap mass spectrometer with three independent ion sources for the study of gas-phase ion/ion reactions

An instrument for the study of gas-phase ion/ion reactions in which three independent sources of ions, namely, two electrospray ionization sources and one atmospheric sampling glow discharge ionization source, are interfaced to a quadrupole ion trap mass analyzer is described. This instrument expands the scope of gas-phase ion/ion reaction studies by allowing for manipulation of the charge states of multiply charged reactant and product ions. Examples are provided involving the formation of protein-protein complexes in the gas phase. Complexes with charge states that cannot be formed from reactant ion charge states present in the normal electrospray charge state distributions can be formed in the new apparatus. Strategies that rely on both reactant ion charge state manipulation and product ion charge state manipulation are demonstrated. In addition, simplification of product ion spectra generated from dissociation of complexes formed via ion/ion reactions can be effected by using the discharge source to reduce the charge state of the product ions to primarily 1+.     

Microplasma mass spectrometric detection in capillary gas chromatography

A simple and miniaturized 350-kHz helium discharge for plasma mass spectrometric detection in gas chromatography (GC) has been developed. The plasma was sustained at low pressure within the end of the capillary GC column (0.32-mm i.d.) inside the ion source housing of a quadrupole mass spectrometer. This allowed direct introduction of ions from the plasma to the mass analyzer using only a repeller and electrostatic lenses to focus the ions. The plasma was sustained in only 25 mL min(-)(1) of helium, which was accepted by the mass spectrometer vacuum system. This low gas flow also served to enhance the energy density of the discharge and to produce a narrow spray of ions toward the mass analyzer. Due to the miniaturized nature of the plasma, it was operated at a low power level (2.0 W), and traces of oxygen were added to avoid deposition of carbon. With this new concept for GC plasma mass spectrometric detection, chlorine was successfully monitored down to the 2.2 pg s(-)(1) level without interference from elements like C, S, P, O, F, and N.