Exact mass measurement of product ions for the structural confirmation and identification of unknown compounds using a quadrupole time-of-flight spectrometer: a simplified approach using combined tandem mass spectrometric functions

This article describes a simple method to perform lock mass corrected accurate mass measurements in tandem mass spectrometry (MS/MS) with a quadrupole time-of-flight (Q-TOF) mass spectrometer. The experimental approach consists of using the protonated molecule of a known compound, which is measured in a MS/MS function using low collision energy (no fragmentation), as mass calibrator. The unknown compound is acquired in MS/MS mode albeit using high collision energy. After the acquisition, the two MS/MS spectra of unknown and mass calibrator are combined, and the fragments of the unknown are lock mass corrected by using the protonated molecule of the mass calibrator. To prove this concept, 10 compounds were analyzed using this approach, the fragments interpreted and, where possible, related to structural data available in the literature. All the unequivocally assigned fragments were accurately mass measured with mass errors within appropriate limits, i.e. for m/z values <200 with a mass tolerance of 3 mDa while for m/z > 200 the mass tolerance is expressed as 10 ppm.     

Comparison of a two-dimensional liquid chromatography/mass spectrometry approach with a chip-based nanoelectrospray device for structural elucidation of metabolites in a human ADME study using a quadrupole time-of-flight mass spectrometer

The study of the metabolic fate of drugs is essential for the safety assessment of new compounds in the drug development process. However, the characterization and structural elucidation of metabolites from in vivo experiments is still a very challenging task. In this paper, we compare a two-dimensional liquid chromatography/mass spectrometry (LC/MS) approach using either a capillary LC/MS system or the recently introduced chip-based nanoelectrospray/MS system (Nanomate) as the second dimension for structural elucidation of metabolites by MS. More than 30 radioactive fractions of a chromatographic separation from a human urine sample were analyzed and 54 metabolites could be identified. The long persisting and stable nanoelectrospray enabled the search for unknown metabolites by precursor-ion scanning experiments followed by product-ion scanning experiments of potential metabolites using a quadrupole time-of-flight (qTOF) mass spectrometer. The number of fragments produced by nanoelectrospray with product-ion scanning was significantly higher compared to LC/MS experiments with in-source fragmentation. Therefore, the assignment of possible modifications in metabolites to certain moieties of the drug could be investigated with higher accuracy. The capillary LC/MS system for the second dimension was more sensitive in the case of low abundant metabolites. These metabolites could not be detected by direct nanoelectrospray infusion, which limits the application of the Nanomate for trace metabolites.     

Evaluation of automated single mass spectrometry to tandem mass spectrometry function switching for comprehensive drug profiling analysis using a quadrupole time-of-flight mass spectrometer

A liquid chromatographic mass spectrometric strategy for systematic toxicological analysis (STA) is presented using the automatic 'on-the-fly' single mass spectrometry mode to tandem mass spectrometry mode (MS to MS/MS) switching abilities of a quadrupole time-of-flight (Q-TOF) instrument. During the chromatographic run, the quadrupole is initially set to transmit all masses until (an) ion(s) reaches a certain set threshold. Thereupon, the quadrupole automatically switches to the MS/MS mode, selecting the ion(s), which are subsequently fragmented in the high-efficiency hexapole collision cell, thus generating product ions that are further mass analyzed by the TOF. By limiting the TOF spectral accumulation time in the MS/MS mode to a statistically acceptable minimum, the quadrupole almost instantly switches back to the MS mode. Qualitative information, comprising the complementary MS ([M + H](+) ion mass) and MS/MS (informative product ion profile) data, as well as quantitative information obtained by integration of the MS extracted ion chromatogram(s), can be obtained in one single acquisition. Optimization of the automatic switching parameters, such as threshold, TOF spectral accumulation time, detection window and collision energy, was carried out by injection of a mix of 17 common drugs which were not necessarily baseline separated in the chromatographic system used. Indeed, the complete separation of the drugs is not deemed necessary since up to 8 different ions can 'simultaneously' be selected for MS/MS if they reach the preset criteria. In addition, the quantitative performance of the method was defined. In a second phase, the developed method was field-tested. To that end, the resulting data from extracts of urine samples were compared with and found to be in close concordance with those obtained by a standard toxicological analysis. This innovative approach clearly holds the potential for a substantial advance in the introduction of LC/MS in STA.     

A collinear tandem time-of-flight mass spectrometer for infrared photodissociation spectroscopy of mass-selected ions

An apparatus based on collinear tandem time-of-flight mass spectrometer has been designed for the measurement of infrared photodissociation spectroscopy of mass-selected ions in the gas phase.The ions from a pulsed laser vaporization supersonic ion source are skimmed and mass separated by a Wiley-McLaren time-of-flight mass spectrometer.The ion of interest is mass selected,decelerated and dissociated by a tunable IR laser.The fragment and parent ions are reaccelerated and mass analyzed by the second time-of-flight mass spectrometer.A simple new assembly integrated with mass gate,deceleration and reacceleration ion optics was designed,which allows us to measure the infrared spectra of mass selected ions with high sensitivity and easy timing synchronization.     

Scanning a triple quadrupole mass spectrometer for doubly charged ions

Charge exchange reactions within a triple quadrupole mass spectrometer characterize doubly charged ions formed in the ion source. Two methods have been developed for identifying the singly charged ions formed from doubly charged ions by charge exchange in the collision quadrupole. The first is based on the characteristically high kinetic energy-to-charge ratios of the products of charge exchange; this property can be used to separate these ions from all other singly charged ions. This retarding potential method is analogous to procedures for recording doubly charged ion mass spectra using sector instruments. The second method is based on the fact that, although mass remains constant in the charge exchange reaction, the change in mass-to-charge ratio can be followed. A charge exchange linked scan, predicated on changes in charge rather than mass, but otherwise analogous to neutral loss/gain scans, is described. Information on the structure of doubly charged ions can be obtained by recording the fragmentation products of dissociative charge exchange. The utility of the charge exchange linked scan for the selective identification of polynuclear aromatic compounds in a complex mixture is described. The methods given can be generalized to cover other charge permutation reactions.     

Charge state separation for protein applications using a quadrupole time-of-flight mass spectrometer

A novel method for separating ions according to their charge state using a quadrupole time-of-flight mass spectrometer is presented. The benefits of charge state separation are particularly apparent in protein identification applications at low femtomole concentration levels, where in conventional TOF MS spectra peptide ions are often lost in a sea of chemical noise. When doubly and triply charged tryptic peptide ions need to be filtered from singly charged background ions, the latter are suppressed by two to three orders of magnitude, while from 10-50% of multiply charged ions remain. The suppression of chemical noise reduces the need for chromatography and can make this experimental approach the electrospray equivalent of conventional MALDI peptide maps. If unambiguous identification cannot be achieved, MS/MS experiments are performed on the precursor ions identified through charge separation, while the previously described Q2-trapping duty cycle enhancement is tuned for approximately 1.4 of the precursor m/z to enhance intensities of ions with m/z values above that of the precursor. The resulting product ion spectra contain few fragments of impurities and provide quick and unambiguous identification through database search. The multiple charge separation technique requires minimal tuning and may become a useful tool for analysis of complex mixtures.     

Combining capillary with radio-frequency-only quadrupole as an interface for a home-made time-of-flight mass spectrometer

A heated capillary tube combined with a radio-frequency-only quadrupole has been coupled with a home- made, high-resolution orthogonal-injection, time-of-flight mass spectrometer to improve ion transmission from the atmospheric pressure to the low--pressure regions. With an electrospray ion source, the performance of the interface on the intensity of spectra was investigated. For electrospray ionization, the ion intensity detected on the time-of- flight mass spectrometer was seen to increase three-fold compared with an orifice interface. It has been shown that the enhanced ion inlet designs can not only increase the ion translation efficiency, but also improve the detection limits of the mass spectrometer. Coupling atmospheric pressure matrix-assisted laser desorption/ionization with the improved interface resulted in an instrument detection limit as low as 2.5 fmol.     

Resolution limitations from detector pulse width and jitter in a linear orthogonal-acceleration time-of-flight mass spectrometer

Recent and ongoing advances in timing electronics together with the development of ionization techniques suited to time-of-flight mass spectrometry (TOF-MS) have contributed to renewed interest in this method of mass analysis. Whereas low resolving powers (m/?m < 500) were once an almost unavoidable drawback in TOF-MS, recent developments in instrument geometries have produced much higher resolving powers for many ion sources. The temporal width of detector pulses and jitter in timing electronics, however, lead to contributions to peak widths that are essentially independent of the mass-analyzer ion optics. The effective detector pulse width (?t _d ≈ 1–10 ns typically) can be a limiting factor in the development of high resolution time-of-flight (TOF) instruments with modest drift lengths (～1 m), It also reduces the mass resolution more seriously for light ions. This article presents a method for distinguishing the instrumental “ion arrival-time” resolution (R _o) of a linear TOF mass analyzer from that which is locally measured at a particular mass, limited by the broadening of the detector pulse width and electronics. The method also provides an estimate of ?t _d, that is useful in determining the temporal performance of the detection system. The model developed here is tested with data from a recently constructed orthogonal-acceleration TOF mass spectrometer equipped with a commercially available transient recorder (a LeCroy 400-Msamplejs digital oscilloscope) from which we obtained R _o = 4240 ± 100 [full width at half maximum (FWHM)) and ?t _d = 3.0 ± 0.1 ns (FWHM).     

A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance

A matrix-assisted laser desorption/ionization (MALDI) source has been coupled to a tandem quadrupole/time-of-flight (QqTOF) mass spectrometer by means of a collisional damping interface. Mass resolving power of about 10,000 (FWHM) and accuracy in the range of 10 ppm are observed in both single-MS mode and MS/MS mode. Sub-femtomole sensitivity is obtained in single-MS mode, and a few femtomoles in MS/MS mode. Both peptide mass mapping and collision-induced dissociation (CID) analysis of tryptic peptides can be performed from the same MALDI target. Rapid spectral acquisition (a few seconds per spectrum) can be achieved in both modes, so high throughput protein identification is possible. Some information about fragmentation patterns was obtained from a study of the CID spectra of singly charged peptides from a tryptic digest of E. coli citrate synthase. Reasonably successful automatic sequence prediction (>90%) is possible from the CID spectra of singly charged peptides using the SCIEX Predict Sequence routine. Ion production at pressures near 1 Torr (rather than in vacuum) is found to give reduced metastable fragmentation, particularly for higher mass molecular ions. Copyright 2000 John Wiley & Sons, Ltd.     

RNA fragmentation studied in a matrix-assisted laser desorption/ionisation tandem quadrupole/orthogonal time-of-flight mass spectrometer

We have studied the fragmentation behaviour of short, singly protonated oligoribonucleotides on a MALDI Qq-TOF instrument with the aim of using this instrumental set-up to characterise modifications of RNA molecules. Individual ion species from enzymatically generated mixtures were isolated in one quadrupole and subjected to collision-induced dissociation in a second quadrupole followed by separation of the resulting product ions in an orthogonal time-of-flight mass analyser. Complex spectra were generally observed with nearly all types of cleavages along the phosphodiester backbone and of the N-glycosidic bonds (and combinations of these) occurring, albeit at different relative intensities. The most labile part of the backbone was found to be the 5'-P-O bond, resulting in c- and y-ions. Loss of neutral cytosine and guanine occurred equally often, whereas neutral loss of adenosine was less prevalent. Loss of uracil, either neutral or charged species, was not observed. Because the fragmentation pattern observed here is significantly different from what has been reported for singly protonated oligodeoxyribonucleotides, we suggest that the 2'-substituent in the sugar plays a central role in the fragmentation mechanisms of nucleic acids. Finally, we used the acquired knowledge about oligoribonucleotide fragmentation to characterise an in vivo methylated oligoribonucleotide by tandem mass spectrometry.     

Coupling a microchip with electrospray ionization quadrupole time-of-flight mass spectrometer for peptide separation and identification

The present study reports a simple method of coupling a glass microchip to an electrospray ionization (ESI) quadrupole time-of-flight mass spectrometer (QTOF-MS) for separation and identification of peptides. A sheath-flow electrospray interface was constructed based on attaching a short fused-silica capillary to the microchip. The dead volume at the interface was effectively reduced by wet etching an approximate flat-bottom capillary insertion channel coaxial to the end of separation microchannel and using a wire-controlled epoxy-blocking attachment method. The makeup liquid and neb gas were coaxially pumped through two stainless-steel tees to maintain a stable and efficient electrospray. The coupled microchip/ESI-QTOF-MS system was successfully used to carry out electrophoresis separation of peptides and ESI-QTOF-MS identification.     

Exact mass measurement on an electrospray ionization time-of-flight mass spectrometer: error distribution and selective averaging

An automated, accurate and reliable way of acquiring and processing flow injection data for exact mass measurement using a bench-top electrospray ionization time-of-flight (ESI-TOF) mass spectrometer is described. Using Visual Basic programs, individual scans were selected objectively with restrictions on ion counts per second for both the compound of interest and the mass reference peaks. The selected "good scans" were then subjected to two different data-processing schemes ("combine-then-center" and "center-then-average"), and the results were compared at various ion count limit settings. It was found that, in general, the average of mass values from individual scans is more accurate than the centroid mass value of the combined (same) scans. In order to acquire a large number of good scans in one injection (to increase the sampling size for statistically valid averaging), an on-line dilution chamber was added to slow down the typically rapid mass chromatographic peak decay in flow-injection analysis. This simple addition worked well in automation without the need for manual sample dilution. In addition, by dissolving the reference compound directly into the mobile phase, manual syringe filling can be eliminated. Twenty-seven samples were analyzed with the new acquisition and process routines in positive electrospray ionization mode. For the best method found, the percentage of samples with RMS error less than 5 ppm was 100% with repetitive injection data (6 injections per sample), and 95% with single injection data. Afterwards, 31 other test samples were run (with MW ranging from 310 to 3493 Da, 21 samples in ESI+ and 10 in ESI- mode) and processed with similar parameters and 100% of them were mass-calculated to RMS error less than 5 ppm also.     

Use of a five-channel multiplexed electrospray quadrupole time-of-flight hybrid mass spectrometer for metabolite identification

Metabolism data provided with reduced cycle time has become of increasing importance for the early evaluation of DMPK properties of drugs in discovery. In this regard, quadrupole time-of-flight hybrid mass spectrometers (Q-TOF) can provide very reliable metabolite identification via accurate mass measurement of ions and the consequent access to the elemental composition of the metabolite. However, due to their cost, they are often used for drug metabolism studies on later stage drug candidates or to address challenging metabolism questions. A new prototype, consisting of a five-channel multiplexed electrospray ionization (ESI) source on a Q-TOF with one channel used for lock-mass compound infusion, was evaluated for metabolite identification. The goal was to increase the sample throughput of a single ESI-MS system by a factor of 4, while maintaining efficient metabolite separation in high-performance liquid chromatography (HPLC) as well as adequate sensitivity and mass accuracy, and ultimately improve the speed and quality of metabolism studies supporting drug discovery. The analytical performance of the system was assessed by evaluating the sensitivity and mass accuracy (using real in vitro and in vivo samples), inter-channel differences in retention times, MS/UV response, and cross-talk among channels. The sensitivity using the multiplexed ESI source was on average 2-fold lower than with single ESI, correlating well with previous literature data. The mass accuracy was comparable to that obtained using single ESI in both MS and MS/MS modes, making the metabolite identification process using the multiplexed ESI source as reliable as with single ESI. Compound-dependent differences in ionization efficiencies were observed among channels, and were minimized by analyzing related samples on the same channel. Finally, the level of cross-talk among channels was acceptable (around 0.3%) and comparable to levels previously published for quantitative applications using multiplexed ESI. The paper also focuses on the advantages and disadvantages of this new approach compared to other approaches in the literature in the field of metabolite identification.     

A tandem time-of-flight mass spectrometer: combination of a multi-turn time-of-flight and a quadratic-field mirror

A tandem time-of-flight (ToF) mass spectrometer consisting of a multi-turn time-of-flight (ToF) and a quadratic-field ion mirror has been designed and constructed. The instrument combines the unique capabilities of both ToF instruments, namely high-resolution and monoisotopic precursor ion selection from the multi-turn ToF and temporal focus for fragment ions with different kinetic energies from the quadratic-field mirror. The first tandem mass spectra for this unique combination of ToF systems are presented.     

Performance optimisation of a new-generation orthogonal-acceleration quadrupole-time-of-flight mass spectrometer

Orthogonal-acceleration quadrupole time-of-flight (oa-QTOF) mass spectrometers, employed for accurate mass measurement, have been commercially available for well over a decade. A limitation of the early instruments of this type was the narrow ion abundance range over which accurate mass measurements could be made with a high degree of certainty. Recently, a new generation of oa-QTOF mass spectrometers has been developed and these allow accurate mass measurements to be recorded over a much greater range of ion abundances. This development has resulted from new ion detection technology and improved electronic stability or by accurate control of the number of ions reaching the detector. In this report we describe the results from experiments performed to evaluate the mass measurement performance of the Bruker micrOTOF-Q, a member of the new-generation oa-QTOFs. The relationship between mass accuracy and ion abundance has been extensively evaluated and mass measurement accuracy remained stable (+/-1.5 m m/z units) over approximately 3-4 orders of magnitude of ion abundance. The second feature of the Bruker micrOTOF-Q that was evaluated was the SigmaFit function of the software. This isotope pattern-matching algorithm provides an exact numerical comparison of the theoretical and measured isotope patterns as an additional identification tool to accurate mass measurement. The smaller the value, the closer the match between theoretical and measured isotope patterns. This information is then employed to reduce the number of potential elemental formulae produced from the mass measurements. A relationship between the SigmaFit value and ion abundance has been established. The results from the study for both mass accuracy and SigmaFit were employed to define the performance criteria for the micrOTOF-Q. This provided increased confidence in the selection of elemental formulae resulting from accurate mass measurements.     

Investigation of the advanced functionalities of a hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometer

Time-of-flight mass spectrometry (ToF-MS) has gained wide acceptance in many fields of chemistry, proteomics, metabolomics and small molecule analysis. ToF-MS, however, has some inherent advantages and drawbacks. Numerous developments have been made to hybrid ToF instruments to improve their capabilities. We have used a quadrupole orthogonal acceleration ToF (Q-oa-ToF) instrument to assess developments made to improve resolution, dynamic range and signal-to-noise (S/N) ratios (i.e. sensitivity). Higher mass resolution can improve the analysis of mixtures containing compounds with similar m/z values and improved mass accuracy gives greater confidence for structural elucidation applications. Wide dynamic ranges are necessary for the analysis of unknown samples or samples that vary widely in analyte concentrations. The performance of the advanced functionalities for routine structural elucidation in terms of resolution, dynamic range and S/N ratios was investigated using test compounds. The results presented in this work demonstrate and validate the use of these new enhancements for Q-ToF instruments and also show their limitations.     

Dual-micro-ESI source for precise mass determination on a quadrupole time-of-flight mass spectrometer for genomic and proteomic applications

A universal dual-electrospray (ESI) source is demonstrated on a quadrupole orthogonal-accelerated time-of-flight mass spectrometer (Q-ToF-MS) for both genomic and proteomic applications. This facile source modification enables internal calibration for consistent mass measurements by a mainstream MS platform and requires no mixing of analyte and calibrant prior to ion formation. In this report, the dual-sprayer is demonstrated in the negative-ion mode for internal calibration of polymerase chain reaction (PCR) amplicons generated from synthetic and genomic templates as well as a proteolytic digest of a naturally phosphorylated protein. For all PCR amplicons, experimentally determined average mass measurements are well within the instrument specifications of better than 0.01%. For the proteolytic fragments of the phosphoprotein, average mass errors of the isotopically resolved peptides are better than 10 ppm.     

Design and performance of a desktop time-of-flight mass spectrometer for analyzing metal ions

We have described a home-made desktop orthogonal-injection time-of-flight (O-ToF) mass spectrometer combining a collisional cooling system. This O-ToF consists of a simple electrospray ion source, an atmosphere-vacuum interface, an area of transmission, including a radio-frequency only quadrupole (RF- only quadrupole, RFQ) as a collisional cooling cell and an orthogonal ToF mass analyzer. In order to detect ions of small m/z value, such as small metal ions, the RFQ has been improved to weaken the mass discrimination effect against low mass ions. Metal salt solutions were used in the experiment. The system has shown a satisfactory resolving power in the spectra (m/Δm = 3500), a good mass stability, a limit of detection of 80 fg and a mass accuracy of 48 ppm. The dynamic range is found to be from 10(-8) mol L(-1) to 10(-5) mol L(-1), allowing the semi-quantitative analysis of metal ions.     

An ion-storage time-of-flight mass spectrometer for analysis of electrospray ions.

A preliminary design and implementation of a novel approach to electrospray-mass spectrometry are described. Based on a time-of-flight mass analysis, the instrument provides several important advantages for on-line mass analysis: 1, simplicity, ease of use and low manufacturing cost; 2, rapid scan speed, yielding quasi-instantaneous full mass scans at repetition rates up to several kHz; 3, soft ionization and accurate mass determination of extremely large analyte molecules; 4, high sensitivity.     

Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer

High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.