MALDI ion trap mass spectrometer with charge detector for large biomolecule detection

Up to now, all commercial matrix-assisted laser desorption/ionization (MALDI) mass spectrometers still can not efficiently analyze very large biomolecules. In this work, we report the development of a novel MALDI ion trap mass spectrometer which can enrich biomolecular ions to enhance the detection sensitivity. A charge detector was installed to measure the large ions directly. With this design, we report the first measurement of IgM with the mass-to-charge ratio (m/z) at 980?000. In addition, quantitative measurements of the number of ions can be obtained. A step function frequency scan was first developed to get a clear signal in the m/z range from 200,000 to 1,000,000.     

Ion trap mass spectrometry of fluorescently labeled nanoparticles

Mass spectra of fluorescently labeled polystyrene nanoparticles have been obtained using a combined technique of matrix-assisted laser desorption/ionization (MALDI), laser-induced fluorescence (LIF), and a dual quadrupole ion trap mass spectrometer. The spectrometer is designed in such a way that the first trap serves as a trapping and mass-analyzing device, while the second trap serves to capture and concentrate the ions ejected from the first trap for fluorescence detection. An enhancement in the LIF signal by more than 3 orders of magnitude is achieved with the help of the second trap, making mass/charge (m/z) analysis of the nanoparticles possible. Additional unique features of this mass spectrometer include that frequency scan (0.5-50 kHz) at a constant voltage (200 V), instead of voltage scan at a constant frequency, is implemented to widen the spectral analysis range of the instrument. The implementation has allowed the spectrometer to operate at relatively high buffer gas pressures (50 mTorr), crucial for effective trapping of the nanometer-sized particles generated by MALDI. We present in this report the first mass spectra of fluorescently labeled nanoparticles with a size of 27 nm using this new mass spectrometric approach. The utility of this method in the study of biological macromolecules or particles is demonstrated with dye-labeled IgG.     

Atmospheric pressure MALDI/ion trap mass spectrometry

A new sample ionization technique, atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI), was coupled with a commercial ion trap mass spectrometer. This configuration enables the application-specific selection of external atmospheric ionization sources: the electrospray/APCI (commercially available) and AP MALDI (built in-house), which can be readily interchanged within minutes. The detection limit of the novel AP MALDI/ion trap is 10-50 fmol of analyte deposited on the target surface for a four-component mixture of peptides with 800-1700 molecular weight. The possibility of peptide structural analysis by MS/MS and MS3 experiments for AP MALDI-generated ions was demonstrated for the first time.     

Fourier transform time-of-flight mass spectrometry in an electrostatic ion beam trap

We report on the application of an electrostatic ion beam trap as a mass spectrometer. The instrument is analogous to an optical resonator; ions are trapped between focusing mirrors. The storage time is limited by the residual gas pressure and reaches up to several seconds, resulting in long ion flight paths. The oscillation of ion bunches between the mirrors is monitored by nondestructive image charge detection in a field-free region and mass spectra are obtained via Fourier transform. The principle of operation is demonstrated by measuring the mass spectrum of trapped Ar+ and Xe+ particles, produced by a standard electron impact ion source. Also, mass spectra of heavier PEGnNa+ and bradykinin ions from a pulsed MALDI ion source were obtained. The long ion flight path, combined with mass-independent charge detection, makes this system particularly interesting for the investigation of large molecules.     

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.     

Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer.

A matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer of new design is described. The instrument is based on a commercial Finnegan LCQ ion trap mass spectrometer to which we have added a MALDI ion source that incorporates a sample stage constructed from a compact disk and a new ion transmission interface. The ion interface contains a quadrupole ion guide installed between the skimmer and the octapoles of the original instrument configuration, allowing for operation in both MALDI and electrospray ionization modes. The instrument has femtomole sensitivity for peptides and is capable of collecting a large number of MALDI MS and MALDI MS/MS spectra within a short period of time. The MALDI source produces reproducible signals for 10(4)-10(5) laser pulses, enabling us to collect MS/MS spectra from all the discernible singly charged ions detected in a MS peptide map. We describe the different modes of the instrument operation and algorithms for data processing as applied to challenging protein identification problems.     

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.     

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.     

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.     

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.     

Linear ion trap for second-order Doppler shift reduction in frequency standard applications

The authors have designed and are presently testing a novel linear ion trap that permits storage of a large number of ions with reduced susceptibility to the second-order Doppler effect caused by the RF confining fields. This new trap should store about 20 times the number of ions as a conventional RF trap with no corresponding increase in second-order Doppler shift from the confining field. In addition, the sensitivity of this shift to trapping parameters, i.e., RF voltage, RF frequency, and trap size, is greatly reduced. The authors have succeeded in trapping mercury ions and xenon ions in the presence of helium buffer gas. Trap times as long as 2x 10(3) s have been measured.     

Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry

A novel ionization source for biological mass spectrometry is described that combines atmospheric pressure (AP) ionization and matrix-assisted laser desorption/ionization (MALDI). The transfer of the ions from the atmospheric pressure ionization region to the high vacuum is pneumatically assisted (PA) by a stream of nitrogen, hence the acronym PA-AP MALDI. PA-AP MALDI is readily interchangeable with electrospray ionization on an orthogonal acceleration time-of-flight (oaTOF) mass spectrometer. Sample preparation is identical to that for conventional vacuum MALDI and uses the same matrix compounds, such as alpha-cyano-4-hydroxycinnamic acid. The performance of this ion source on the oaTOF mass spectrometer is compared with that of conventional vacuum MALDI-TOF for the analysis of peptides. PA-AP MALDI can detect low femtomole amounts of peptides in mixtures with good signal-to-noise ratio and with less discrimination for the detection of individual peptides in a protein digest. Peptide ions produced by this method generally exhibit no metastable fragmentation, whereas an oligosaccharide ionized by PA-AP MALDI shows several structurally diagnostic fragment ions. Total sample consumption is higher for PA-AP MALDI than for vacuum MALDI, as the transfer of ions into the vacuum system is relatively inefficient. This ionization method is able to produce protonated molecular ions for small proteins such as insulin, but these tend to form clusters with the matrix material. Limitations of the oaTOF mass spectrometer for singly charged high-mass ions make it difficult to evaluate the ionization of larger proteins.     

MALDI of individual biomolecule-containing airborne particles in an ion trap mass spectrometer

Individual airborne biomolecule-containing particles were detected and characterized in near real-time by matrix-assisted laser desorption/ionization (MALDI) with an ion trap mass spectrometer. Biomolecule-containing particles were laboratory-generated and passed through a heated region containing a solution of matrix in equilibrium with the gas phase. Passage into a cooler region created a supersaturation, resulting in rapid deposition of the matrix vapor onto the biomolecule-containing particles, whereupon they were sampled into the inlet of our spectrometer. The coated particles were collimated and individually sized by light-scattering-based time-of-flight. When the sized particle reached the center of the ion trap, it was irradiated with a focused 266-nm laser, and the resulting ions were mass-analyzed. Mass spectra of leucine enkephalin, bradykinin, substance P, and polylysine-containing particles were determined with attomole sensitivity. Structural information of the peptides contained in an individual particle was obtained by tandem mass spectrometry. Analysis of the results yields insights into the aerosol laser ablation ionization process that suggests an optically limited mechanism for ion production that has interesting ramifications on the utility of aerosol-based MALDI as an analytical technique.     

Narrow-band collisional activation technique for ion trap mass spectrometers.

Narrow-bandwidth signals were applied to the end caps of an ion trap mass spectrometer to excite ions during collisional activation. Excitation waveforms were created from a single-frequency component and a random noise component using a multiplier circuit. Tandem and higher order mass spectrometry experiments (MS3) can be performed without optimization of the supplemental frequency applied to the end cap electrodes. The usefulness of this method of ion excitation is demonstrated using singly and multiply protonated peptide ions as well as sodium-cationized carbohydrates.     

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.     

Analysis of VX on soil particles using ion trap secondary ion mass spectrometry.

The direct detection of the nerve agent VX (methylphosphonothioic acid, S-[2-[bis(1-methylethyl)amino]ethyl] O-ethyl ester) on milligram quantities of soil particles has been achieved using ion trap secondary ion mass spectrometry (IT-SIMS). VX is highly adsorptive toward a wide variety of surfaces; this attribute makes detection using gas-phase approaches difficult but renders the compound very amenable to surface detection. An ion trap mass spectrometer, modified to perform SIMS, was employed in the present study. A primary ion beam (ReO4-) was fired on axis through the ion trap, where it impacted the soil particle samples. [VX + H]+, [VX + H]+ fragment ions, and ions from the chemical background were sputtered into the gas-phase environment of the ion trap, where they were either scanned out or isolated and fragmented (MS2). At a surface concentration of 0.4 monolayer, intact [VX + H]+, and its fragment ions, were readily observable above background. However, at lower concentrations, the secondary ion signal from VX became obscured by ions derived from the chemical background on the surface of the soil particles. MS2 analysis using the ion trap was employed to improve detection of lower concentrations of VX: detection of the 34S isotopic ion of [VX + H]+, present at a surface concentration of approximately 0.002 monolayer, was accomplished. The study afforded the opportunity to investigate the fragmentation chemistry of VX. Semiempirical calculations suggest strongly that the molecule is protonated at the N atom. Deuterium labeling showed that formation of the base peak ion (C2H4)N(i-C3H7)2+ involves transfer of the amino proton to the phosphonothioate moiety prior to, or concurrent with, C-S bond cleavage. To manage the risk associated with working with the compound, the vacuum unit of the IT-SIMS was located in a hood, connected by cables to the externally located electronics and computer.     

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.     

Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract

A linear octopole trap interface for an ion mobility time-of-flight mass spectrometer has been developed for focusing and accumulating continuous beams of ions produced by electrospray ionization. The interface improves experimental efficiencies by factors of approximately 50-200 compared with an analogous configuration that utilizes a three-dimensional Paul geometry trap (Hoaglund-Hyzer, C. S.; Lee, Y. J.; Counterman, A. E.; Clemmer, D. E. Anal. Chem. 2002, 74, 992-1006). With these improvements, it is possible to record nested drift (flight) time distributions for complex mixtures in fractions of a second. We demonstrate the approach for several well-defined peptide mixtures and an assessment of the detection limits is given. Additionally, we demonstrate the utility of the approach in the field of proteomics by an on-line, three-dimensional nano-LC-ion mobility-TOF separation of tryptic peptides from the Drosophila proteome.     

New paradigm in ionization: multiply charged ion formation from a solid matrix without a laser or voltage

Laserspray ionization (LSI) is a new approach to producing multiply charged ions from solids on surfaces by laser ablation of matrixes commonly used in matrix-assisted laser desorption/ionization (MALDI). We show that the only necessity of the laser for producing multiply charged ions is to deliver particles or droplets of the matrix/analyte mixture to an ionization zone which is simply a heated inlet to the vacuum of the mass spectrometer. Several other methods for delivering sample are demonstrated to produce nearly equivalent results. One example shows the use of an air gun replacing the laser and producing mass spectra of proteins by shooting pellets into a metal plate which has matrix/analyte applied to the opposite side and near the ion entrance inlet to the mass spectrometer. Multiply charged ions of proteins are produced in the absence of any electric field or laser and with only the need of a heated ion entrance capillary or skimmer. The commonality of the matrix with MALDI and the mild conditions necessary for formation of ions brings into question the mechanism of formation of multiply charged ions and the importance of matrix structure in this process.     

Internal calibration on adjacent samples (InCAS) with Fourier transform mass spectrometry

Using matrix-assisted laser desorption/ionization (MAL DI) on a trapped ion mass spectrometer such as a Fourier transform mass spectrometer (FTMS) allows accumulation of ions in the cell from multiple laser shots prior to detection. If ions from separate MALDI samples are accumulated simultaneously in the cell, ions from one sample can be used to calibrate ions from the other sample. Since the ions are detected simultaneously in the cell, this is, in effect, internal calibration, but there are no selective desorption effects in the MALDI source. This method of internal calibration with adjacent samples is demonstrated here on cesium iodide clusters, peptides, oligosaccharides, poly(propylene glycol), and fullerenes and provides typical FTMS internal calibration mass accuracy of < 1 ppm.