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.     

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.     

Ion transport diagnostics in a microsecond pulsed Grimm-type glow discharge time-of-flight mass spectrometer

A Grimm-type glow discharge ion source, operated in the microsecond pulsed mode, has been interfaced to a commercial time-of-flight mass spectrometer. Ion transport from the source to the mass spectrometer, an inherent limitation of a Grimm source and mass spectrometer combination, was evaluated. The primary discharge operating conditions found to influence transport efficiency were gas flow rate and source pressure. The configuration of the Grimm-type source also influenced ion transport, including use of a gas-directing sleeve device. The effect of transport efficiency was separated into two components: (1) total ion signal and (2) temporal resolution. The latter is an advantage afforded by use of a pulsed glow discharge source and time-of-flight spectrometer, which allows discrimination against interfering gaseous background ions by appropriate ion sampling time. Shown as an example is the identification of trace magnesium from potential background interference using an optimized source configuration based on this temporal resolution method.     

Investigation of the unusual behavior of metolachlor under chemical ionization in a hybrid 3D ion trap mass spectrometer

This article describes the strange behavior of the widely used herbicide metolachlor under chemical ionization conditions in a hybrid source ion trap mass spectrometer in gas chromatography/mass spectrometry (GC/MS) coupling. With the use of ammonia as the reagent gas, metolachlor provides a chlorinated ion at m/z 295/297, almost as abundant as the protonated molecule at m/z 284/286, which cannot be isolated to perform tandem mass spectrometry (MS(n)) experiments. Curiously, this ion at m/z = M + 12 is not observed for the herbicides acetochlor and alachlor, which present very similar chemical structures. The chemical structure of the m/z 295/297 ions and the explanation of the observed phenomenon based on the metastable behavior of these ions were elucidated on the basis of experiments including isotopic labeling and modifications of the operating conditions of the ion trap mass spectrometer. This work allows one to give new recommendations for an optimized use of hybrid source ion trap mass spectrometers.     

Broad-band fourier transform quadrupole ion trap mass spectrometry

Broad-band nondestructive ion detection is achieved in a quadrupole ion trap mass spectrometer by impulsive excitation of a collection of trapped ions of different masses and recording of ion image currents induced on a small detector electrode embedded in but isolated from the adjacent end cap electrode. The image currents are directly measured using a simple differential preamplifier, filter, and amplifier combination and then Fourier analyzed to obtain broad-band frequency domain spectra characteristic of the sample ions. The use of the detector electrode provides a significant reduction in capacitive coupling with the ring electrode. This minimizes coupling of the rf drive signal, which can saturate the front-end stage of the detection circuit and prevent measurement of the relatively weaker ion image currents. Although impulsive excitation is preferred due to its broad-band characteristics and simplicity of use, results are also given for narrow-band ac and broad-band SWIFT (stored wave-form inverse Fourier transform) excitation. Data using argon, acetophenone, and n-butylbenzene show that a resolution of better than 1000 is obtained with a detection bandwidth of 400 kHz. An advantage of nondestructive ion detection is the ability to measure a single-ion population multiple times. This is demonstrated using argon as the sample gas with an average remeasurement efficiency of >90%. Tandem mass spectrometry experiments using a population of acetophenone ions are also shown.     

Non-proximate detection of small and large molecules by desorption electrospray ionization and desorption atmospheric pressure chemical ionization mass spectrometry: instrumentation and applications in forensics, chemistry, and biology

Ambient surfaces are examined by mass spectrometry at distances of up to 3 m from the instrument without any prior sample preparation. Non-proximate versions of the desorption electrospray ionization (DESI) and desorption atmospheric pressure chemical ionization experiments are shown to allow rapid, sensitive, and selective detection of trace amounts of active ingredients in pharmaceutical drug formulations, illicit drugs (methamphetamine, cocaine, and diacetylmorphine), organic salts, peptides, chemical warfare agent simulants, and other small organic compounds. Utilizing an ion transport tube to transport analyte ions to the mass spectrometer, nonproximate DESI allows one to collect high-quality, largely interference-free spectra with signal-to-noise (S/N) ratios of more than 100. High selectivity is achieved by tandem mass spectrometry and by reactive DESI, a variant experiment in which reagents added into the solvent spray allow bond-forming reactions with the analyte. Ion/molecule reactions were found to selectively suppress the response of mixture components other than the analyte of interest in nonproximate-DESI. Flexible ion transport tubing is also investigated, allowing performance similar to stainless steel tubing in the transport of ions from the sample to the mass spectrometer. Transfer tube temperature effects are examined. A multiple sprayer DESI source capable of analyzing a larger sample area was evaluated to decrease the sampling time and increase sample throughput. Low nanogram detection limits were obtained for the compounds studied from a wide variety of surfaces, even those present in complex matrixes.     

Independent control of ion transmission in a jet disrupter dual-channel ion funnel electrospray ionization MS interface

A new atmospheric pressure ionization mass spectrometer (API-MS) interface has been developed to allow the control of ion transmission through the first vacuum stage of the mass spectrometer. The described interface uses a dual-heated capillary and a dual-inlet ion funnel design. Two electrosprays, aligned with the dual-capillary inlet, are used to introduce ions from different solutions independently into the MS. The initial design was specifically aimed at developing a method for the controlled introduction of calibrant ions in highly accurate mass measurements using Fourier transform ion cyclotron resonance mass spectrometer (FTICR). The dual-channel ion funnel has different inlet diameters that are aligned with the dual capillaries. The large diameter main channel of the ion funnel is used for analyte introduction to provide optimum ion transmission. The second, smaller diameter channel inlet includes a jet disrupter in the ion funnel to modulate the ion transmission through the channel. The two inlet channels converge into a single-channel ion funnel where ions from both channels are mixed, focused, and transmitted to the mass analyzer. Both theoretical simulations and experimental results show that the transmission of different m/z species in the small diameter channel of the ion funnel can be effectively modulated by varying the bias voltage on the jet disrupter. Both static and dynamic modulations of ion transmission are demonstrated experimentally by applying either a constant DC or a square waveform voltage to the jet disrupter. High ion transmission efficiency, similar to the standard single-channel ion funnel, is maintained in the main analyte channel inlet of the ion funnel over a broad m/z range with negligible "cross talk" between the two ion funnel inlet channels. Several possible applications of the new interface (e.g., for high-accuracy MS analysis of complex biological samples) are described.     

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.     

Ion-exchange chromatography/electrospray mass spectrometry for the identification of organic and inorganic species in topiramate tablets

An ion-exchange chromatograph/electrospray ionization mass spectrometer (IC/ESI-MS) was used successfully to identify organic and inorganic species present in topiramate tablets. An ion suppressor is placed between the column and detectors to replace sodium ions in the mobile phase with hydrogen ions supplied by the suppressor. The ensuing combination of the hydrogen ions with the mobile phase hydroxide ions produces water and thus allows simultaneous ion detection by an ion conductivity detector and a mass spectrometer. Analytes, including lactate, glycolate, chloride, formate, sulfate, and oxalate, were unambiguously identified by matching the mass spectra and retention times with those of the authentic compounds. Due to its capability of detecting positive and negative as well as neutral species, ESI-MS provides valuable information which is not available with ion conductivity detection alone. Though the coupling of ion-exchange chromatography to mass spectrometry has been reported previously, this is the first demonstration of IC/ESI-MS for the identification of unknown species in real samples. Finally, with the use of deuterium/carbon-13 labeling and MS/MS techniques, we have confirmed that oxalic acid (HOOC-COOH) is formed from formic acid (HCOOH) at the electrospray interface in the presence of the electric field. This observation not only confirms the identity of an unknown peak, but it also provides new insight into chemistry that can take place during electrospray ionization.     

Design and performance of an instrument for soft landing of biomolecular ions on surfaces

A new ion deposition apparatus was designed and constructed in our laboratory. Our research objectives were to investigate interactions of biomolecules with hydrophilic and hydrophobic surfaces and to carry out exploratory experiments aimed at highly selective deposition of spatially defined and uniquely selected biological molecules on surfaces. The apparatus includes a high-transmission electrospray ion source, a quadrupole mass filter, a bending quadrupole that deflects the ion beam and prevents neutral molecules originating in the ion source from impacting the surface, an ultrahigh vacuum (UHV) chamber for ion deposition by soft landing, and a vacuum lock system for introducing surfaces into the UHV chamber without breaking vacuum. Ex situ analysis of surfaces following soft landing of mass-selected peptide ions was performed using 15 keV Ga+ time-of-flight secondary ion mass spectrometry and grazing incidence infrared reflection-absorption spectroscopy. It is shown that these two techniques are highly complementary methods for characterization of surfaces prepared with a range of doses of mass-selected biomolecular ions. We also demonstrated that soft landing of peptide ions on surfaces can be utilized for controlled preparation of peptide films of known coverage for fundamental studies of matrix effects in SIMS.     

Infrared multiphoton dissociation for quantitative shotgun proteomics

We modified a dual-cell linear ion trap mass spectrometer to perform infrared multiphoton dissociation (IRMPD) in the low-pressure trap of a dual-cell quadrupole linear ion trap (dual-cell QLT) and perform large-scale IRMPD analyses of complex peptide mixtures. Upon optimization of activation parameters (precursor q-value, irradiation time, and photon flux), IRMPD subtly, but significantly, outperforms resonant-excitation collisional-activated dissociation (CAD) for peptides identified at a 1% false-discovery rate (FDR) from a yeast tryptic digest (95% confidence, p = 0.019). We further demonstrate that IRMPD is compatible with the analysis of isobaric-tagged peptides. Using fixed QLT rf amplitude allows for the consistent retention of reporter ions, but necessitates the use of variable IRMPD irradiation times, dependent upon precursor mass to charge (m/z). We show that IRMPD activation parameters can be tuned to allow for effective peptide identification and quantitation simultaneously. We thus conclude that IRMPD performed in a dual-cell ion trap is an effective option for the large-scale analysis of both unmodified and isobaric-tagged peptides.     

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.     

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.     

SIMS and GDMS depth profile analysis of hard coatings

Rapid development in hard coating technology calls for simple construction depth profile analysers. Here we present results of depth profile analysis of a set of Ar arc plasma deposited TiN, CrN layers. The results are obtained with the use of recently constructed simple glow discharge mass spectrometer (GDMS) and compared with secondary ion mass spectrometer (SIMS). In SIMS (SAJW-05 model) we apply 5 keV Ar⁺ ion beam of about 100 μm in diameter. Digitally controlled spiral scanning of primary ion beam is performed over 1.6 mm² area. Secondary ions are extracted from the central part due to an “electronic gate” and analysed by quadrupole mass spectrometer QMA-410 Balzers (16 mm rods).GDMS analyses are performed on SMWJ-01 glow discharge prototype spectrometer. To supply discharge in 1 hPa argon we use 1.5 kV DC voltage. The analysed sample works as a cathode in a discharge cell. Area of the analysis is ∼4 mm² due to the use of secondary cathode—high purity tantalum diaphragm. Sputtered atoms are ionised, next extracted into the analytical chamber and finally analysed by the quadrupole mass analyser SRS-200 (6 mm rods).The results show that the use of simple construction GDMS analyser allows obtaining similar or even slightly better depth resolution than it can be obtained in the SIMS spectrometer. Application of glow discharge analysis opens new possibilities in direct quantitative depth profile analysis of hard coatings.     

Frequency-scanning MALDI linear ion trap mass spectrometer for large biomolecular ion detection

This study presents the first report on the development of a matrix-assisted laser desorption ionization (MALDI) linear ion trap mass spectrometer for large biomolecular ion detection by frequency scan. We designed, installed, and tested this radio frequency (RF) scan linear ion trap mass spectrometer and its associated electronics to dramatically extend the mass region to be detected. The RF circuit can be adjusted from 300 to 10 kHz with a set of operation amplifiers. To trap the ions produced by MALDI, a high pressure of helium buffer gas was employed to quench extra kinetic energy of the heavy ions produced by MALDI. The successful detection of the singly charged secretory immunoglobulin A ions indicates that the detectable mass-to-charge ratio (m/z) of this system can reach ~385 000 or beyond.     

An automated matrix-assisted laser desorption/ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometer for "bottom-up" proteomics

Here we describe a new quadrupole Fourier transform ion cyclotron resonance hybrid mass spectrometer equipped with an intermediate-pressure MALDI ion source and demonstrate its suitability for "bottom-up" proteomics. The integration of a high-speed MALDI sample stage, a quadrupole analyzer, and a FT-ICR mass spectrometer together with a novel software user interface allows this instrument to perform high-throughput proteomics experiments. A set of linearly encoded stages allows sub-second positioning of any location on a microtiter-sized target with up to 1536 samples with micrometer precision in the source focus of the ion optics. Such precise control enables internal calibration for high mass accuracy MS and MS/MS spectra using separate calibrant and analyte regions on the target plate, avoiding ion suppression effects that would result from the spiking of calibrants into the sample. An elongated open cylindrical analyzer cell with trap plates allows trapping of ions from 1000 to 5000 m/z without notable mass discrimination. The instrument is highly sensitive, detecting less than 50 amol of angiotensin II and neurotensin in a microLC MALDI MS run under standard experimental conditions. The automated tandem MS of a reversed-phase separated bovine serum albumin digest demonstrated a successful identification for 27 peptides covering 45% of the sequence. An automated tandem MS experiment of a reversed-phase separated yeast cytosolic protein digest resulted in 226 identified peptides corresponding to 111 different proteins from 799 MS/MS attempts. The benefits of accurate mass measurements for data validation for such experiments are discussed.     

Thermally assisted collision-induced dissociation in a quadrupole ion trap mass spectrometer

Thermally assisted collision-induced dissociation (TA-CID) provides increased dissociation in comparison with CID performed at ambient temperature in a quadrupole ion trap mass spectrometer. Heating the bath/collision gas during CID increases the initial internal energy of the ions and reduces the collisional cooling rate. Thus, using the same CID parameters, the parent ion can be activated to higher levels of internal energy, increasing the efficiency of dissociation and the number of dissociation pathways. The increase in the number of dissociation pathways can provide additional structural information. A consequence of the increase in initial internal energy is the ability to use less power to effect collisional activation. This allows lower q(z) values to be used and, thus, a greater mass range of product ions to be observed. TA-CID alleviates the problems associated with traditional CID and results in more available information than traditional CID.     

Partial currents of ion species in an expanding laser-created plasma

A novel analysis of ion currents, which is based on the use of shifted Maxwell-Boltzmann velocity distribution, is applied to quantify the properties of expanding laser-produced plasmas into the vacuum. The ion currents were measured outside the critical zone where the recombination and collisional excitation processes are not important and the charge-states of ions are frozen. The deconvolution of single-shot ion currents is applied for recovering the partial currents of participating ion species in the measured ion currents in carbon, copper and polyethylene plasmas created by various pulsed laser beams. This method allows determining the plasma temperature, the centre-of-mass velocities of individual charge-states and their abundance. The obtained charge-state dependencies of the centre-of-mass velocities render important details in establishing the mechanisms responsible for the ion emission, which has fundamental importance in applications of laser ion sources.     

High-throughput miniature cylindrical ion trap array mass spectrometer

A fully multiplexed cylindrical ion trap (CIT) array mass spectrometer with four parallel ion source/mass analyzer/detector channels has been built to allow simultaneous high-throughput analysis of multiple samples. A multielement external chemical ionization/electron ionization source was coupled to a parallel array of CITs each of equal size (internal radius 2.5 mm), and the signal was recorded using an array of four miniature (2-mm inner diameter) electron multipliers. Using external electron ionization, the spectra of four separate samples were recorded simultaneously in real time using a four-channel preamplifier system and a data acquisition program written using LabVIEW software. These experiments mark the first demonstration of externally generated ions being successfully trapped in a miniature CIT mass analyzer. The instrument currently provides mass/charge range of approximately m/z 50-500. Average peak width is m/z 0.3, corresponding to a resolution of 1000 at m/z 300. The four-channel mass spectrometer is housed in a single vacuum manifold and operated with a single set of control electronics. The modular design of this instrument allows scale-up to many more channels of analysis for future applications in the areas of industrial process monitoring and combinatorial analysis and in the fields of proteomics and metabolomics.