Enhanced ion utilization efficiency using an electrodynamic ion funnel trap as an injection mechanism for ion mobility spectrometry

Conventional ion mobility spectrometers that sample ion packets from continuous sources have traditionally been constrained by an inherently low duty cycle. As such, ion utilization efficiencies have been limited to <1% in order to maintain instrumental resolving power. Using a modified electrodynamic ion funnel, we demonstrated the ability to accumulate, store, and eject ions in conjunction with ion mobility spectrometry (IMS), which elevated the charge density of the ion packets ejected from the ion funnel trap (IFT) and provided a considerable increase in the overall ion utilization efficiency of the IMS instrument. A 7-fold increase in signal intensity was revealed by comparing continuous ion beam current with the amplitude of the pulsed ion current in IFT-IMS experiments using a Faraday plate. Additionally, we describe the IFT operating characteristics using a time-of-flight mass spectrometer attached to the IMS drift tube.     

Interfacing the orbitrap mass analyzer to an electrospray ion source

The orbitrap mass analyzer employs the trapping of pulsed ion beams in an electrostatic quadro-logarithmic field. This field is created between an axial central electrode and a coaxial outer electrode. Stable ion trajectories combine rotation around the central electrode with harmonic oscillations along it. The frequencies of axial oscillations and hence mass-to-charge ratios of ions are obtained using fast Fourier transform of the image current detected on the two split halves of the outer electrode. This work proves that such a trap could be coupled to a continuous, electrospray, ion source. Such a coupling necessitated the development of an rf-only quadrupole for external accumulation of ions and their injection in very short (< 1 micros) ion bunches. Along with good sensitivity, this mass spectrometer provides mass resolving power up to 150,000 fwhm, mass accuracies within a few parts per million, and relative mass range up to 8-fold. The maximum number of ions available for analysis is limited by the space-charge capacity of the accumulation quadrupole.     

An interface with a linear quadrupole ion guide for an electrospray-ion trap mass spectrometer system

A new ion sampling interface for an electrospray ionization 3D ion trap mass spectrometer system is described. The interface uses linear rf quadrupoles as ion guides and ion traps to enhance the performance of the 3D trap. Trapping ions in the linear quadrupoles is demonstrated to improve the duty cycle of the system. Dipolar excitation of ions trapped in a linear quadrupole is used to eject unwanted ions. A resolution of ejection of up to 254 is demonstrated for protonated reserpine ions (m/z 609.3). A composite waveform with a notch in frequency space is used to eject a wide range of matrix ions and to isolate trace analyte ions in a linear quadrupole before ions are injected into the 3D trap. This is useful to overcome space charge problems in the 3D trap caused by excess matrix ions. For trace reserpine in a 500-fold molar excess of poly(propylene glycol) (PPG), it is demonstrated that the resolution and sensitivity of the 3D trap can be increased dramatically with ejection of the excess PPG matrix ions. In comparison to ejection of matrix ions in the 3D trap with a similar broad-band waveform, a 5-fold increase in sensitivity with a 7 times shorter acquisition time was achieved.     

Coaxial ion trap mass spectrometer: concentric toroidal and quadrupolar trapping regions

We present the design and results for a new radio-frequency ion trap mass analyzer, the coaxial ion trap, in which both toroidal and quadrupolar trapping regions are created simultaneously. The device is composed of two parallel ceramic plates, the facing surfaces of which are lithographically patterned with concentric metal rings and covered with a thin film of germanium. Experiments demonstrate that ions can be trapped in either region, transferred from the toroidal to the quadrupolar region, and mass-selectively ejected from the quadrupolar region to a detector. Ions trapped in the toroidal region can be transferred to the quadrupole region using an applied ac signal in the radial direction, although it appears that the mechanism of this transfer does not involve resonance with the ion secular frequency, and the process is not mass selective. Ions in the quadrupole trapping region are mass analyzed using dipole resonant ejection. Multiple transfer steps and mass analysis scans are possible on a single population of ions, as from a single ionization/trapping event. The device demonstrates better mass resolving power than the radially ejecting halo ion trap and better sensitivity than the planar quadrupole ion trap.     

Transmission mode ion/ion electron-transfer dissociation in a linear ion trap

Two related methods for effecting electron-transfer dissociation (ETD) are described that involve either the storage of analyte cations in a linear ion trap while reagent anions are transmitted through the cations or storage of the reagent anions with transmission of the analyte cations. In the former approach, the ETD products are captured and stored in the linear ion trap for subsequent mass analysis. In the latter approach, the ETD products pass through the linear ion trap and must be collected or directly mass-analyzed by an external device. In the present study, another linear ion trap is placed in series with the ion trap where the ion/ion reaction was employed. A pulsed dual ion source approach coupled with a hybrid triple quadrupole/linear ion trap instrument was used to illustrate these methods. The two approaches give similar results in terms of the identities and relative abundances of the ETD products. Under optimum conditions, the two approaches also give comparable extents of ion/ion reactions for the same reaction time. Also, conversions of precursor ions to product ions over the same reaction time are similar to those noted for experiments in which ions of both polarities are stored simultaneously. These approaches, therefore, provide expanded experimental options for the use of ETD. An advantage of transmission mode experiments that they hold over mutual storage mode experiments is that they do not require that any specialized measures be taken to enable the simultaneous storage of oppositely charged ions.     

Automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry

Time-of-flight mass spectrometry (TOF MS) is increasingly used in proteomics research. Herein, we report on the development and characterization of a TOF MS instrument with improved sensitivity equipped with an electrodynamic ion funnel trap (IFT) that employs an automated gain control (AGC) capability. The IFT-TOF MS was coupled to a reversed-phase capillary liquid chromatography (RPLC) separation and evaluated in experiments with complex proteolytic digests. When applied to a global tryptic digest of Shewanella oneidensis proteins, an order-of-magnitude increase in sensitivity compared to that of the conventional continuous mode of operation was achieved due to efficient ion accumulation prior to TOF MS analysis. As a result of this sensitivity improvement and related improvement in mass measurement accuracy, the number of unique peptides identified in the AGC-IFT mode was 5-fold greater than that obtained in the continuous mode.     

Dynamic pressure measurements during pulsed gas injection in a quadrupole ion trap

A quadrupole ion trap has been modified to perform dynamic pressure measurements during pulsed introduction of gases. A continuous electron beam is directed through the ion trap where the gas is ionized via electron impact. Ion and electron currents are monitored on the ring and end-cap electrodes, respectively. Dynamic pressure measurements in a region not accessible to a standard gauge are performed using a static quadrupole field. Characteristic current-voltage curves of the ion-trap gauge are presented and optimum operating conditions of the electron-ion optical system are identified in steady state conditions. The sensitivity of the ion-trap gauge is calibrated at these optimum conditions. In the pulsed gas mode ion and electron signals are measured simultaneously on a fast oscilloscope. The time constant of the circuit for the dynamic measurements is ∼129 μs and pressure variations of ∼10⁻⁴-1 Pa occur within 60-130 ms. The exponential decay of the ion signals is used to calculate pumping speeds for helium and argon gases. The distinctive advantages of pulsed gas injections over the use of static pressures in quadrupole ion-trap mass spectrometry are emphasized.     

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.     

Tandem ion trap design with enhanced mass analysis capabilities for large populations of ions

A new arrangement consisting of two separate radio frequency (rf) quadrupole ion traps is used to analyze large populations of ions over a wide mass-to-charge (m/z) range. The setup consists of an "accumulation" trap that is maintained at a higher pressure than the second high-performance "analyzer" trap. The two traps are scanned simultaneously, with a mass difference between that determines the residence time and mass range of ions in the analytical trap. Initially, all ions are trapped in the accumulation trap and then mass-selectively ejected into the analyzer trap. As ions arrive in the analyzer trap, they cool through collisions with the buffer gas and then are mass selectively ejected toward the detector. This concurrent linked mass scanning reduces the total number of ions present in the analyzer trap during mass analysis, thereby reducing space charge effects and leading to improved resolution and mass accuracy of analytical spectra.     

Ion trap/ion mobility/quadrupole/time-of-flight mass spectrometry for peptide mixture analysis

An ion trap/ion mobility/quadrupole/time-of-flight mass spectrometer has been developed for the analysis of peptide mixtures. In this approach, a mixture of peptides is electrosprayed into the gas phase. The mixture of ions that is created is accumulated in an ion trap and periodically injected into a drift tube where ions separate according to differences in gas-phase ion mobilities. Upon exiting the drift tube, ions enter a quadrupole mass filter where a specific mass-to-charge (m/z) ratio can be selected prior to collisional activation in an octopole collision cell. Parent and fragment ions that exit the collision cell are analyzed using a reflectron geometry time-of-flight mass spectrometer. The overall configuration allows different species to be selected according to their mobilities and m/z ratios prior to collision-induced dissociation and final MS analysis. A key parameter in these studies is the pressure of the target gas in the collision cell. Above a critical pressure, the well-defined mobility separation degrades. The approach is demonstrated by examining a mixture of tryptic digest peptides of ubiquitin.     

VUV single-photon ionization ion trap time-of-flight mass spectrometer for on-line, real-time monitoring of chlorinated organic compounds in waste incineration flue gas

In this work, a sensitive and robust vacuum ultra-violet (VUV) single-photon ionization (SPI) ion trap time-of-flight mass spectrometer (VUV-SPI-IT-TOFMS) for on-line, realtime monitoring of chlorinated organic compounds in waste incineration flue gas has been newly developed. The fragment-free SPI technique with 121.6-nm VUV lamp irradiated by a microwave generator and the quadrupole ion trap to accumulate and select analyte ions were combined with a reflectron time-of-flight mass spectrometer to detect chlorinated organic compounds at trace level. This measuring system was tuned up to detect dioxins precursors with the aim at an application to monitoring trace level toxic substances in flue gases from incinerator furnaces. As a result, this technology has made it possible to analyze trichlorobenzene (T3CB), a dioxin precursor, in 18 s with a sensitivity of 80 ng/m3-N (10 pptv) using the selective accumulation of analyte substances and separation of interfering substances in the ion trap. Moreover, the first field test of the continuous monitoring T3CB in an actual waste incineration flue gas had been done for 7 months. The results show that this system has an exceeding robust performance and is able to maintain the high sensitivity in analyzing T3CB for long months of operation.     

Electrospray Ion Chromatography-Tandem Mass Spectrometry of Bromate at Sub-ppb Levels in Water

An electrospray ion chromatography-tandem mass spectrometry (IC-MS/MS) method has been developed for the analysis of bromate ions in water. This IC-MS/MS method improves the limit of detection of bromate ions by a factor of 10. The method consists of solid phase extraction with an ion exchange column and elution of the analyte with water/methanol ammonium sulfate eluent on-line with a negative ion electrospray mass spectrometry detection. SPE requires sample pretreatment to remove any major ions that displace bromate, consisting of eliminating SO(4)(2)(-), Cl(-), and HCO(3)(-) ions respectively with barium-form, silver-form, and acid (H(+)-form) exchange resins. The methanolic sulfate eluent permits IC-MS coupling via an electrospray interface. BrO(3)(-) was selected in the first quadrupole (Q1) at two m/z values, 127 and 129, according to the isotope contributions of (79)Br and (81)Br. After fragmentation in the collision cell (second quadrupole, Q2), the third quadrupole (Q3) analyzes the product ions as (M - O)(-), (M - 2O)(-), and (M - 3O)(-). Among the six recordable transitions, four were selected, the other two yielding high background. A lowered resolution raised sensitivity by a factor of up to 3. The limit of quantitation of this method was 0.1 μg/L.     

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.     

Investigation of the rapid scan on an electrospray ion trap mass spectrometer

A rapid scan on a quadrupole ion trap mass spectrometer can improve the signal intensity by over 200 times when scanning at 12 times the normal scan rate. This intensity increase is due to a 5.5-fold increase in mass peak height due to a reduction in the mass peak width over time and a 40-fold increase in signal from the increased number of ions that can be trapped without the deleterious effects of space charge. Detection limits can be further improved by signal averaging more scans in the same period that is required for the normal scan, and the greatest advantage occurs when scanning over the full mass range. The rapid scan impacts the mass accuracy and the resolution is reduced by 6 times. The molecular weight determination of 40 fmol/microL apomyoglobin was determined in 3 s using a rapid scan, but this was not possible when using the normal scan rate. Quantitation results showed that the relative standard deviations for the total ion current peak areas of 500 fmol of angiotensin I were improved by a factor of 2.6 when the rapid scan was used.     

Charge determination of product ions formed from collision-induced dissociation of multiply protonated molecules via ion/molecule reactions.

The use of ion/molecule reactions involving multiply protonated ions derived from electrospray for the determination of the charges of product ions formed from collision-induced dissociation is described. The experiments are carried out with a quadrupole ion trap capable of multiple stages of mass spectrometry. The approach is illustrated with proton transfer from a product ion from quadruply protonated melittin, and from a product ion from the (M + 20H)20+ ion from horse myoglobin, to 1,6-diaminohexane. The major product ion from quadruply protonated bovine insulin is used to illustrate the use of a clustering reaction with 1,6-diaminohexane. The ion trap is shown to be a particularly useful tool for employing both collisional activation and low-energy ion/molecule reactions in the same experiment to determine product ion charge.     

Oligonucleotide mixture analysis via electrospray and ion/ion reactions in a quadrupole ion trap

Electrospray ionization combined with ion/ion reactions in a quadrupole ion trap can be used for the direct analysis of oligonucleotide mixtures. Elements to the success of this approach include factors related to ionization, ion/ion reactions, and mass analysis. This paper deals with issues regarding the ion polarity combination, viz., positive oligonucleotides/negative charge-transfer agent versus negative oligonucleotides/positive charge-transfer agent. Anions derived from perfluorocarbons appear to be directly applicable to mixtures of positive ions derived from electrospray of oligonucleotides, in direct analogy with positive protein ions. Conditions for forming positive oligonucleotide ions devoid of adducts were more difficult to establish than for forming relatively clean negative oligonucleotide ions. A new approach for manipulating negative ion charge states in the ion trap is described and is based on use of the electric field of the positive charge-transfer agent for storage of high-mass negative ions formed during the ion/ion reaction period. Oxygen cations are shown to be acceptable for charge-state manipulation of mixed-base oligomers but induce fragmentation in polyadenylate homopolymers. Protonated isobutylene (C4H9+), on the other hand, is shown to induce significantly less fragmentation of polyadenylate homopolymers.     

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.     

High resolution time-of-flight mass analysis of the entire range of intact singly-charged proteins

The proof of principle for high-resolution analysis of intact singly charged proteins of any size is presented. Singly charged protein ions were produced by electrospray ionization followed by surface-induced charge reduction at atmospheric pressure. The inlet and trapping system "stops" the forward momentum of the protein ions over a very broad range to be captured by the digitally produced electric fields of a large radius linear ion trap whereupon they are moved into a smaller radius linear ion trap and collected and concentrated in front of its exit end-cap electrode using digital waveform manipulation. The protein ions are then ejected on demand from the end of the small radius linear quadrupole in a tightly collimated ion beam with an instrumentally defined kinetic energy into the acceleration region of an orthogonal acceleration reflectron time-of-flight mass analyzer where their flight times were measured and detected with a Photonis BiPolar TOF detector. We present results that clearly prove that massive singly charged ions can yield high-resolution mass spectra with very low chemical noise and without loss of sensitivity with increasing mass across the entire spectrum. Analysis of noncovalently bound protein complexes was demonstrated with streptavidin-Cy5 bound with a biotinylated peptide mimic. Our results suggest proteins across the entire range can be directly quantified using our mass analysis technique. We present evidence that solvent molecules noncovalently adduct onto the proteins while yielding consistent flight time distributions. Finally, we provide a look into future that will result from the ability to rapidly measure and quantify protein distributions.     

High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 Tesla

We describe the design and current performance of a 14.5 T hybrid linear quadrupole ion trap Fourier transform ion cyclotron resonance mass spectrometer. Ion masses are routinely determined at 4-fold better mass accuracy and 2-fold higher resolving power than similar 7 T systems at the same scan rate. The combination of high magnetic field and strict control of the number of trapped ions results in external calibration broadband mass accuracy typically less than 300 ppb rms, and a resolving power of 200,000 (m/Delta m50% at m/z 400) is achieved at greater than 1 mass spectrum per second. Novel ion storage optics and methodology increase the maximum number of ions that can be delivered to the FTICR cell, thereby improving dynamic range for tandem mass spectrometry and complex mixture applications.     

Collisional activation with random noise in ion trap mass spectrometry.

Random noise applied to the end caps of a quadrupole ion trap is shown to be an effective means for the collisional activation of trapped ions independent of mass/charge ratio and number of ions. This technique is compared and contrasted with conventional single-frequency collisional activation for the molecular ion of N,N-dimethylaniline, protonated cocaine, the molecular anion of 2,4,6-trinitrotoluene, and doubly pronated neuromedin U-8. Collisional activation with noise tends to produce more extensive fragmentation than the conventional approach due to the fact that product ions are also kinetically excited in the noise experiment. The efficiency of the noise experiment in producing detectable product ions relative to the conventional approach ranges from being equivalent to being a factor of 3 less efficient. Furthermore, discrimination against low mass/charge product ions is apparent in the data from multiply charged biomolecules. Nevertheless, collisional activation with random noise provides a very simple means for overcoming problems associated with the dependence of single-frequency collisional activation on mass/charge ratio and the number of ions in the ion trap.