A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics

A new hybrid electrospray quadrupole Fourier transform mass spectrometry (FTMS) instrument design is shown and characterized. This instrument involves coupling an electrospray source and mass-resolving quadrupole, ion accumulation, and collision cell linear ion trap system developed by MDS Sciex with a home-built ion guide and ion cyclotron resonance (ICR) cell. The iterative progression of this design is shown. The final design involves a set of hexapole ion guides to transfer the ions from the accumulation/collision trap through the magnetic field gradient and into the cell. These hexapole ion guides are separated by a thin gate valve and two conduction limits to maintain the required <10(-9) mbar vacuum for FTICR. Low-attomole detection limits for a pure peptide are shown, 220 000 resolving power in broadband mode and 820 000 resolving power in narrow-band mode are demonstrated, and mass accuracy in the <2 ppm range is routinely available provided the signal is abundant, cleanly resolved, and internally calibrated. This instrument design provides high experimental flexibility, allowing Q2 CAD, SORI-CAD, IRMPD, and ECD experiments with selected ion accumulation as well as experiments such as nozzle skimmer dissociation. Initial top-down mass spectrometry experiments on a protein is shown using ECD.     

MS3 using the collision cell of a tandem mass spectrometer system

We report the feasibility of multistage fragmentation in combination with a fast background subtraction method, yielding the equivalent of MS3. The first quadrupole selects an ion of interest, and the ion is axially accelerated into Q2 to generate fragment ions. Subsequent stages of mass selection and fragmentation are obtained by quadrupolar resonant excitation within the Q2 collision cell. The fragments are analyzed downstream by either a resolving quadrupole or a time-of-flight (TOF) mass spectrometer, and multistage spectra are obtained by subtraction (MS(n) - MS(n-1)) for n = 3 or 4. We discuss the characterization of this method, including product ion arrival times, fragmentation efficiencies, and ion selectivity. We report accurate TOF mass spectra of background-subtracted MS3 for protonated molecules reserpine (m/z 609), bosentan (m/z 1552), and taxol (m/z 854).     

High-performance liquid chromatography-tandem mass spectrometry with a new quadrupole/linear ion trap instrument

The use of a new hybrid quadrupole/linear ion trap known as the Q TRAP offers unique benefits as a LC-MS-MS detector for both small and large molecule analyses. The instrument combines the capabilities of a triple quadrupole mass spectrometer and ion trap technology on a single platform. Product ion scans are conducted in a hybrid fashion with the fragmentation step accomplished via acceleration into the collision cell followed by trapping and mass analysis in the Q3 linear ion trap. This results in triple quadrupole fragmentation patterns with no inherent low molecular mass cutoff. In-trap fragmentation is also possible in order to provide triple MS (MS3) capabilities. There are also several scan modes that are not possible on conventional instruments that enable identification of analytes within complex biological matrixes for subsequent high sensitivity product ion scans. This report will describe the new hybrid instrument and the principles of operation, and also provide examples of the unique scan modes and capabilities of the Q TRAP for LC-MS-MS detection in metabolism identification.     

A Quadrupole mass spectrometer for resolution of low mass isotopes

The qualitative and quantitative identification of low mass isotopes in the mass range 1–6 u poses certain difficulties when attempting to achieve the required resolution with an instrument suitable for deployment within a process environment. Certain adjacent species present in the process sample (HT and D₂) require a resolution greater than 930 to achieve an accurate measurement. We demonstrate here through simulation techniques that this level of performance required is unachievable using commercially available instruments. Using previously reported simulation techniques, this article demonstrates how the required performance for resolving the low mass isotopes can be achieved by a quadrupole mass spectrometer (QMS), which incorporates a quadrupole mass filter (QMF) constructed from hyperbolic electrodes and operated in zone 3 of the Mathieu stability diagram.     

A novel tandem quadrupole mass spectrometer allowing gaseous collisional activation and surface induced dissociation.

A novel tandem quadrupole mass spectrometer is described that enables gaseous collision-induced dissociation (CID) and surface-induced dissociation (SID) experiments. The instrument consists of a commercially available triple quadrupole mass spectrometer connected to an SID region and an additional, orthogonal quadrupole mass analyser. The performance of the instrument was evaluated using leucine-enkephalin, allowing a comparison between CID and SID, and with previous reports of other SID instruments. The reproducibility of SID data was assessed by replicate determinations of the collision energy required for 50% dissociation of leucine-enkephalin; excellent precision was observed (standard deviation of 0.6 eV) though, unexpectedly, the reproducibility of the equivalent figure for CID was superior. Several peptides were analysed using SID in conjunction with liquid secondary-ion mass spectrometry or electrospray; a comparison of the fragmentation of singly protonated peptide ions and the further dissociation of y-type fragments was consistent with the equivalence of the latter fragments to protonated peptides. Few product ions attributable to high-energy cleavages of amino acid side-chains were observed. The SID properties were investigated of a series of peptides differing only in the derivatization of a cysteine residue; similar decomposition efficiencies were observed for all except the cysteic acid analogue, which demonstrated significantly more facile fragmentation.     

Electrospray-assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins

We have constructed an electrospray-assisted laser desorption/ionization (ELDI) source which utilizes a nitrogen laser pulse to desorb intact molecules from matrix-containing sample solution droplets, followed by electrospray ionization (ESI) post-ionization. The ELDI source is coupled to a quadrupole ion trap mass spectrometer and allows sampling under ambient conditions. Preliminary data showed that ELDI produces ESI-like multiply charged peptides and proteins up to 29 kDa carbonic anhydrase and 66 kDa bovine albumin from single-protein solutions, as well as from complex digest mixtures. The generated multiply charged polypeptides enable efficient tandem mass spectrometric (MS/MS)-based peptide sequencing. ELDI-MS/MS of protein digests and small intact proteins was performed both by collisionally activated dissociation (CAD) and by nozzle-skimmer dissociation (NSD). ELDI-MS/MS may be a useful tool for protein sequencing analysis and top-down proteomics study, and may complement matrix-assisted laser desorption/ionization (MALDI)-based measurements.     

Product ion scanning using a Q-q-Q linear ion trap (Q TRAP) mass spectrometer

The use of a Q-q-Q(linear ion trap) instrument to obtain product ion spectra is described. The instrument is based on the ion path of a triple quadrupole mass spectrometer with Q3 operable as either a conventional RF/DC quadrupole mass filter or a linear ion trap mass spectrometer with axial ion ejection. This unique ion optical arrangement allows de-coupling of precursor ion isolation and fragmentation from the ion trap itself. The result is a high sensitivity tandem mass spectrometer with triple quadrupole fragmentation patterns and no inherent low mass cut-off. The use of the entrance RF-only section of the instrument as accumulation ion trap while the linear ion trap mass spectrometer is scanning enhances duty cycles and results in increased sensitivities by as much as a factor of 20. The instrument is also capable of all of the triple quadrupole scans including multiple-reaction monitoring (MRM) as well as precursor and constant neutral loss scanning. The high product ion scanning sensitivity allows the recording of useful product ion spectra near the MRM limit of quantitation.     

Construction of a hybrid quadrupole/fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa

Technological advancements including an open-cylindrical Penning trap with capacitively coupled ICR cell, selective ion accumulation with a resolving quadrupole, and a voltage gradient used during ion extraction from an octopole ion trap, have individually improved dynamic range and sensitivity in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). Documented here is a new instrument utilizing these technologies toward the robust detection and fragmentation of biomolecules >10 kDa. Up to 55-fold enhancement in ion population by selective ion accumulation combined with 10- to 20- fold signal-to-noise improvement by application of a DC voltage gradient to an accumulation octopole during the ion transfer event offers improved signal-to-noise (or speed) of MS/MS experiments, for proteins from Methanococcus jannaschii and Saccharomyces cerevisiae whole cell lysates. After external quadrupole filtering with a 40 m/z window, three proteins were fragmented (and identified) in parallel from the database of Methanococcus jannaschii. Electron capture dissociation (ECD) of an intact yeast protein provides extensive sequence information resulting in a high degree of localization for an N-terminal acetylation. Hybrid fragmentation, infrared multiphoton dissociation (IRMPD) followed by low energy electrons (ECD), with the electron source located laterally off the z-axis and external to the magnet bore, presents a strategy for identification of proteins by means of the sequence tag approach. Automated implementation of diverse MS(n) approaches in a Q-FTMS instrument promises to help realize "top-down" proteomics in the future.     

A double quadrupole for mass spectrometry/mass spectrometry

A double quadrupole mass spectrometer has been constructed to study unimolecular and collision-induced dissociation products from mass-selected ions. The two quadrupoles are closely coupled and the dissociation products sampled from a 2.5-mm interquadrupole region. Spectra obtained on the double quadrupole instrument are compared with published data obtained with triple quadrupole and reversed-sector (MIKE) mass spectrometers. The results indicate that the simple double quadrupole spectrometer is a highly efficient device which is a viable alternative to more complex quadrupole or sector instruments for obtaining dissociation spectra of mass-selected ions.     

Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of non-steroidal antiinflammatory drugs in surface water by liquid chromatography/tandem mass spectrometry

A triple-quadrupole instrument and a hybrid quadrupole/time-of-flight (TOF) mass spectrometer were compared for the determination of pharmaceutical compounds in water samples. The drugs investigated were the analgesics Ibuprofen, Fenoprofen, Ketoprofen, Naproxen, and Diclofenac. The recently introduced Q2-pulsing function, which enhances the transmission of fragment ions of a selected m/z window from the collision cell into the TOF analyzer, improved the sensitivity of product ion scans on the quadrupole/TOF instrument. The selectivity is much better on quadrupole/TOF systems than on triple quadrupoles because the high resolving power of the reflectron-TOF mass analyzer permits high-accuracy fragment ion selection. This minimizes interferences from environmental matrices and allows acquisition of full spectra for selected analytes with better signal-to-noise characteristics than comparable spectra obtained with a scanned quadrupole. The qualitative information obtained (mass accuracy, resolution and full-scan spectra) by hybrid quadrupole/TOF mass spectrometry allows a more certain identification of analytes in environmental matrices at trace levels. Sample enrichment of water samples was achieved by a solid-phase extraction procedure. Average recoveries for loading 1 L of samples varied from 88 to 110%, and the quantification limits were less than 1.2 ng/L for the triple-quadrupole instrument (in MRM mode) and less than 3 ng/L for the quadrupole/TOF instrument.     

Hybrid triple quadrupole-linear ion trap mass spectrometry in fragmentation mechanism studies: application to structure elucidation of buspirone and one of its metabolites

The use of a hybrid triple quadrupole-linear ion trap (QqQ(LIT)) mass spectrometer system for a comprehensive study of fragmentation mechanisms is described. The anxiolytic drug, buspirone, was chosen as a model compound for this study. With the advent of a QqQ(LIT) instrument, both the traditional quadrupole and the new linear ion trap scans (LIT) could be performed in a single LC run. In the past, a sample had to be run on two different instruments, namely, a triple quadrupole instrument (QqQ) and a 3D ion trap (3D IT) to obtain similar information. With the new QqQ(LIT) technology, collision-induced dissociation (CID) occur in a quadrupole collision cell, q2, and fragment ions are trapped and analyzed in Q3 operated in LIT mode. In this work, high-sensitivity product ion spectra of buspirone were obtained from the one-stage 'Enhanced Product Ion' scan (EPI) with rich product ions and no low mass cut-off. Furthermore, detailed fragmentation pathways were elucidated by further dissociation of each of the fragment ions in the EPI spectrum using MS(3) mode in the same run. The MS(3) scan was performed by incorporating CID in q2, and trapping, cooling, isolation, and resonance-excitation in Q3 when operating in LIT mode. This approach allowed unambiguous assignment of all fragment ions quickly with fewer experiments and easier interpretation than the previous approach. The overall sensitivity for obtaining complete fragment ion data was significantly improved for QqQ(LIT) as compared with that of QqQ and 3D IT mass spectrometers. This is beneficial for structure determination of unknown trace components. The method allowed structure determination of metabolites of buspirone in rat microsomes at 1 microM concentration, which was a 10-fold lower concentration than was needed for QqQ or 3D IT instruments. The QqQ(LIT) instrument provided a simple, rapid, sensitive and powerful approach for structure elucidation of trace components.     

Collision-induced fragmentation pathways including odd-electron ion formation from desorption electrospray ionisation generated protonated and deprotonated drugs derived from tandem accurate mass spectrometry

The rapid desorption electrospray ionisation (DESI) of some small molecules and their fragmentation using a triple-quadrupole and a hybrid quadrupole time-of-flight mass spectrometer (Q-ToF) have been investigated. Various scanning modes have been employed using the triple-quadrupole instrument to elucidate fragmentation pathways for the product ions observed in the collision-induced dissociation (CID) spectra. Together with accurate mass tandem mass spectrometry (MS/MS) measurements performed on the hybrid Q-ToF mass spectrometer, unequivocal product ion identification and fragmentation pathways were determined for deprotonated metoclopramide and protonated aspirin, caffeine and nicotine. Ion structures and fragmentation pathway mechanisms have been proposed and compared with previously published data. The necessity for elevated resolution for the differentiation of isobaric ions are discussed.     

High mass selectivity for top-down proteomics by application of SWIFT technology

Stored waveform inverse Fourier transform (SWIFT) technology has been implemented on a commercial Fourier transform ICR mass spectrometer. Complex ejection/isolation waveforms can be generated on an arbitrary waveform generator (AWG) and applied to the instrument by use of a high speed analog switch. High mass selectivity and subsequent electron capture dissociation (ECD) of the SWIFT isolated ions has been demonstrated with analysis of intact Bovine histone H4. A mass selectivity about 0.1 m/z unit for isolation of the 18+ charge state ions was achieved. Adaptation of SWIFT on the commercial instrument provides an enhanced capability for characterizing intact proteins by top-down analysis.     

Furofuranic glycosylated lignans: a gas-phase ion chemistry investigation by tandem mass spectrometry

Alkali metal cation adducts, [M+Alk](+), and [M-H](-) ions of four known glycosylated furofuran lignans, (+)-pinoresinol 4-O-beta-D-glucopyranoside, (+)-phylliroside, (+)-8-hydroxypinoresinol 4-O-beta-D-glucopyranoside, and (+)-8-hydroxypinoresinol 8-O-beta-D-glucopyranoside, recently isolated from Carex distachya, were generated by electrospray ionization and allowed to undergo collisionally activated dissociation (CAD) in a quadrupole ion trap (QIT) and in a triple quadrupole (TQ) mass spectrometer. CAD mass spectra of [M+Na](+) and [M+Li](+) adducts revealed the presence of structurally diagnostic product ions. CAD mass spectra of deprotonated glycosylated furofuran lignans showed the typical neutral loss of 162 Da when the glucose residue was bound to a phenolic oxygen atom. When glycosylation occurred at an alcoholic oxygen, as for (+)-8-hydroxypinoresinol 8-O-beta-D-glucopyranoside, a neutral loss of 180 Da represented the main fragmentation pathway. Selective hydrogen/deuterium (H/D) exchange of all the acidic hydrogen atoms of furofuran glycosides, performed by introducing lignan glycosides in D(2)O/CH(3)OD solutions, were employed to obtain information on the nature of the product ions generated during TQ/CAD processes. Energy-resolved TQ/CAD mass spectra of deprotonated lignan glycosides and their deprotonated aglycones were used in a qualitative way to infer information on the integrated energetic picture of CAD fragmentations and to investigate the mechanism of the predominant dissociation/isomerization processes. On the basis of the hypothesized fragmentation mechanisms, gas-phase features of the furofuran ring were derived. The presence of an OH substituent in the C8 position decreased the electron density in the adjacent C8' position, modifying the fragmentation pathway.     

High mass accuracy in-source collision-induced dissociation tandem mass spectrometry and multi-step mass spectrometry as complementary tools for fragmentation studies of quaternary ammonium herbicides

Fragmentation studies using both an ion-trap mass analyzer and a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer were performed in order to establish the fragmentation pathways of organic molecules. A general strategy combining MSn data (n = 1-4) in an ion-trap analyzer with tandem mass spectrometry and in-source collision-induced dissociation tandem mass spectrometry (CID MS/MS) in a Q-TOF instrument was applied. The MSn data were used to propose a tentative fragmentation pathway following genealogical relationships. When several assignments were possible, MS/MS and in-source CID MS/MS (Q-TOF) allowed the elemental compositions of the fragments to be confirmed. Quaternary ammonium herbicides (quats) were used as test compounds and their fragmentation pathways were established. The elemental composition of the fragments was confirmed using the TOF analyzer with relative errors <0.0023 Da. Some fragments previously reported in the literature were reassigned taking advantage of the high mass resolution and accuracy of the Q-TOF instrument, which made it possible to solve losses where nitrogen was involved.     

Transmission mode ion/ion reactions in the radiofrequency‐only ion guide of hybrid tandem mass spectrometers

Transmission mode ion/ion reactions have been performed within the first quadrupole, the Q0 radiofrequency (RF)‐only quadrupole, of two types of hybrid tandem mass spectrometers (viz., triple quadrupole/linear ion trap and QqTOF instruments). These transmission mode reactions involved the storage of either the reagent species and the transmission of the analyte species through the Q0 quadrupole for charge inversion reactions or the storage of the analyte ions and transmission of the reagent ions as in charge reduction experiments. A key advantage to the use of transmission mode ion/ion reactions is that they do not require any instrument hardware modifications to provide interactions of oppositely charged ions and can be implemented in any instrument that contains a quadrupole or linear ion trap. The focus of this work was to investigate the potential of using the RF‐only quadrupole ion guide positioned prior to the first mass‐resolving element in a tandem mass spectrometer for ion/ion reactions. Two types of exemplary experiments have been demonstrated. One involved a charge inversion reaction and the other involved a charge reduction reaction in conjunction with ion parking. Ion/ion reactions proved to be readily implemented in Q0 thereby adding significantly greater experimental flexibility in the use of ion/ion reaction experiments with hybrid tandem mass spectrometers. Copyright © 2009 John Wiley & Sons, Ltd.     

A comparison of accurate mass techniques for the structural elucidation of fluconazole

Mass spectrometry plays a major role in the structural elucidation and characterisation of drug candidates and related substances. Accurate mass data allow the mathematical prediction of molecular formula of both precursor and fragment ions. In this paper, a comparison of the accurate mass data obtained for the fragmentation of fluconazole, an antifungal drug, by three different methods is made: electron ionisation (EI) using a magnetic sector instrument; electrospray ionisation (ES) using a Fourier transform ion cyclotron mass spectrometer (FTICRMS); and ES using a quadrupole-time-of-flight mass spectrometer (Q-ToF). It is clear from the data obtained that mass accuracy is not simply a function of instrument resolution. The subtle differences observed between collisionally activated dissociation (CAD) and sustained off-resonance collisionally activated dissociation (SORI-CAD) spectra are explained as a consequence of the excitation process. The advantages and disadvantages of the three techniques are discussed within the context of structural elucidation.     

Application of the statistical test of equivalent pathways (STEP) method to the triple quadrupole mass spectrometer

Recently, we demonstrated a new method, STEP (Statistical Test of Equivalent Pathways) analysis, which differentiates first-generation product ions (primary product ions) from second-generation product ions (secondary product ions) obtained in tandem mass spectrometric (MS/MS) experiments on a quadrupole ion trap mass spectrometer. The study presented here defines how to adapt the STEP method to a more routinely used mass analyzer, the triple quadrupole. New ion activation conditions were developed to adapt the STEP method to the triple quadrupole mass spectrometer using peptides and carbohydrates. The application of this method to the triple quadrupole is useful because it provides an efficient approach to differentiate primary and secondary ions on this instrument. Out of the total number of ions that were subjected to the STEP analysis, this method correctly identified 96% of ions as primary or secondary, indicating that this analysis is effective for carbohydrates and peptides undergoing collision-induced dissociation (CID) on a triple quadrupole mass spectrometer.     

Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules

Recently, linear ion traps (LITs) have been combined with quadrupole (Q), time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). LITs can be used either as ion accumulation devices or as commercially available, stand-alone mass spectrometers with MSn capabilities. The combination of triple quadrupole MS with LIT technology in the form of an instrument of configuration QqLIT, using axial ejection, is particularly interesting, because this instrument retains the classical triple quadrupole scan functions such as selected reaction monitoring (SRM), product ion (PI), neutral loss (NL) and precursor ion (PC) while also providing access to sensitive ion trap experiments. For small molecules, quantitative and qualitative analysis can be performed using the same instrument. In addition, for peptide analysis, the enhanced multiply charged (EMC) scan allows an increase in selectivity, while the time-delayed fragmentation (TDF) scan provides additional structural information. Various methods of operating the hybrid instrument are described for the case of the commercial Q TRAP (AB/MDS Sciex) and applications to drug metabolism analysis, quantitative confirmatory analysis, peptides analysis and automated nanoelectrospray (ESI-chip-MS) analysis are discussed.     

Comparison of collisionally activated dissociation mass spectra for the identification of cyclopeptides and cyclodepsipeptides

Collisionally activated dissociation (CAD) spectra of protonated molecules of cyclopeptides and cyclodepsipeptides obtained with two different mass spectrometry systems were compared. Fragmentations were obtained either from collisions induced in the ion source of an electrospray mass spectrometer fitted with a single quadrupole by increasing the extracting cone voltage or from collisions with an inert gas in a free-field area of a fast-atom bombardment (FAB) mass spectrometer. Similar fragmentation pathways were produced with the two configurations even though actual tandem mass spectrometry experiments with magnetic and electric sectors provided more information than cone-induced dissociations. However, only the latter mode allowed us to perform mass spectrometric analyses coupled to liquid chromatography (LC/ESI-MS) at low cost on commercially widespread instruments. Copyright © 1999 John Wiley & Sons, Ltd.