A combined linear ion trap time-of-flight system with improved performance and MS(n) capabilities

A Conjoined Rectilinear Collision Cell and Pulsed Extraction Ion Trap with Auxiliary DC Electrodes

Ion traps are routinely directly coupled to mass analyzers, where they serve to suitably cool and shape an ion population prior to pulsed extraction into the analyzer proper. Such devices benefit from high duty cycle and transmission but suffer slow ion processing times caused by a compromise in the buffer gas pressure range that suitably dampens the ion kinetic energy without causing excessive scatter during extraction or within the analyzer. A rectilinear RF quadrupole ion trap has been characterized, conjoining a pressurized collision region with a pumped extraction region, and an unbroken RF interface for seamless ion transfer between them. Auxiliary electrodes mounted between the RF electrodes provide DC voltage gradients that serve to both guide ions through the device and position them at the extraction slot. The influence of the auxiliary DC upon the trapping RF field was measured, and suitable parameters were defined. A mode of operation was developed that allowed parallel processing of ions in both regions, enabling a repetition rate of 200 Hz when the device was coupled to a high-resolution accurate-mass analyzer.

Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code

The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.

Dual roles of drug or its metabolite-protein conjugate: Cutting-edge strategy of drug discovery using shotgun proteomics

Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug-protein conjugates or metabolite-protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.

Challenges, Progress and Promises of Impurities Annotation for LCMSIT- TOF

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Analysis of pharmaceutical products, as well as their active and inactive ingredients, and identification and characterization of potential impurities originating from raw materials and manufacturing processes is of importance in the field, especially for further assessment of potential positive or negative effects on the human body. In addition to expected therapeutic effects, unfortunately, some unwanted or adverse effects were encountered in the past, resulting in dramatic cases sometimes. These challenges have been overcome with the use of sophisticated and high-end analytical techniques today by focusing on developing more efficient, more accurate, more accessible, and faster determination techniques.

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One of the powerful techniques utilized under the given aim, especially for qualitative purposes, is the Time of Flight (TOF) based Mass Spectrometry (MS). Among the TOF-MS instruments, liquid chromatography- mass spectrometry-ion trap-time of flight (LCMS-IT-TOF) has a unique MSn capability, which is a versatile tool in exact mass prediction and structure elucidation. In this review, LCMS-ITTOF has been considered taking all aspects to account for its use in qualitative impurity profiling, and a retrospective view on previous studies was presented in an analytical manner.

"Lipidomics": Mass spectrometric and chemometric analyses of lipids

Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.

Effect of Transition-Metal Ions on the Conformation of Encephalin Investigated by Hydrogen/Deuterium Exchange and Theoretical Calculations

We have studied the effects of different 3d orbitals in divalent transition-metal ions [G²⁺ = Mn²⁺ (d⁵), Fe²⁺ (d⁶), Co²⁺ (d⁷), Ni²⁺ (d⁸), Cu²⁺ (d⁹), or Zn²⁺ (d¹⁰)] on the conformations of leucine encephalin (LE) and methionine encephalin (ME) in the gas phase using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and theoretical calculations at the molecular level. The HDX-MS reveals a 1:1 stoichiometric monovalent complex of [LE/ME + G - H]⁺ and observed that the different HDX reactivities follow the trend Fe²⁺ < Co²⁺ < Ni²⁺ < Mn²⁺ < Cu²⁺ ≈ Zn²⁺ and that [ME + Mn/Cu/Zn - H]⁺ > [LE + Mn/Cu/Zn - H]⁺, while [LE + Fe/Co/Ni - H]⁺ > [ME + Fe/Co/Ni - H]⁺. We cross-correlated the collision-induced dissociation energies of the complexes with the HDX results and found that the more stable the complex, the harder it is for it to undergo HDX. Furthermore, we used theoretical calculations to optimize the favorable conformations of the complexes and found the same interaction structure of G²⁺ coordination with the five carbonyl oxygens of LE/ME that have different bond lengths. Finally, we calculated the proton affinity (PA) values of the optimized complexes in order to interpret the HDX observations that the higher the PA values, the more difficult it is for the complex to undergo HDX. Overall, both the experiments and the theoretical calculations show that the six metal ions have different effects on the LE/ME conformation, with the low-energy stability of the G²⁺ 3d orbitals corresponding to more dramatic effects on the LE/ME conformation. In addition, the hardness of the ionic acid corresponding to the fully filled Mn²⁺ and half-filled Zn²⁺ orbitals also contributes strongly to the coordination effect; the conformation effect of Fe²⁺/Co²⁺/Ni²⁺ on LE is greater than that on ME, whereas the conformation effect of Mn²⁺/Cu²⁺/Zn²⁺ on ME is greater than that on LE.

Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection

More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora's box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.

Antibiotic analysis using Electro-Filtering Paper Spray Ionization

In this work, we analyzed the performance of the Electro-Filtering Paper Spray Ionization (EFSI) method for detecting compounds in unprocessed samples. A relatively rigid and electrically conductive copper filter was used as a substrate to insure sufficient and efficient sample-solvent extraction and to increase the conductivity for paper spraying. The method was demonstrated as applicable for indirect high-throughput analysis of large-volume unprocessed samples, which is not possible with conventional nanoESI or direct paper spray methods. The new method can generate different desired ion signals for a wide range of compounds by selecting different extraction solvents. Moreover, key parameters related to extraction efficiency were optimized in detail to obtain the most satisfactory extraction efficiency during antibiotic analysis. Finally, under optimal conditions, the EFSI method was successfully used to detect four antibiotics in animal products of egg, chicken, and chicken liver, exhibiting good reproducibility with calibration curves between 81.6% and 96.3%, and R² values above 0.99. Recoveries of 75.0%ￚ94.6% were obtained for the four antibiotics. Hence, the proposed EFSI-MS is a successful, economical, rapid, and high-throughput method that is effective for both unknown and targeted extraction of unprocessed samples by mass spectrometric analysis.

An ion trap time-of-flight mass spectrometer with high mass resolution for cold trapped ion experiments

Trapping molecular ions that have been sympathetically cooled with laser-cooled atomic ions is a useful platform for exploring cold ion chemistry. We designed and characterized a new experimental apparatus for probing chemical reaction dynamics between molecular cations and neutral radicals at temperatures below 1 K. The ions are trapped in a linear quadrupole radio-frequency trap and sympathetically cooled by co-trapped, laser-cooled, atomic ions. The ion trap is coupled to a time-of-flight mass spectrometer to readily identify product ion species and to accurately determine trapped ion numbers. We discuss, and present in detail, the design of this ion trap time-of-flight mass spectrometer and the electronics required for driving the trap and mass spectrometer. Furthermore, we measure the performance of this system, which yields mass resolutions of m/Δm ≥ 1100 over a wide mass range, and discuss its relevance for future measurements in chemical reaction kinetics and dynamics.

Performance assessment of a portable mass spectrometer using a linear ion trap operated in non-scanning mode

RATIONALE

The desire for mass spectrometer portability provides the motivation for simpler, lighter electronics to deliver switched potentials applied to the electrodes of the linear ion trap operated in non-scanning mode. Using a novel method of modelling and theoretical analysis, we simulate the mass analyser performance under these unfavourable operating conditions.

METHODS

The electrical fields are simulated using the Charge Particle Optics software which employs the boundary element method. The ion trajectories are computed from the ion cage of the EI source to the interior of the trap where the ions are confined. The spatial/temporal ion distributions during injection are calculated from the individual ion trajectories computed with constant time-steps. Due to geometric non-linearities, β_y  = 0 lines close to the apex of the stability diagram have been computed for different initial positions with zero initial velocities in order to define the acceptable maximum axial extension.

RESULTS

The DC potential well depth has been estimated at about 15 eV from the axial velocity distribution, and the minimum time of ion injection at 120 μs from the temporal ion distribution. To ensure a mass separation of one unit and the confinement of the whole of the injected ions, buffer gas cooling is necessary to reduce the trajectory excursion amplitudes to 0.1 and 15 mm in the radial and axial directions, respectively.

CONCLUSIONS

The portable mass spectrometer is predicted to achieve a mass resolution of better than one mass unit providing that helium buffer gas is used. An additional cooling sequence has to be added prior to moving the operating point toward the apex. Copyright © 2016 John Wiley & Sons, Ltd.

Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response

The simultaneous detection of all the post-transcriptional modifications (PTMs) that decorate cellular RNA can provide comprehensive information on the effects of changing environmental conditions on the entire epitranscriptome. To capture this type of information, we performed the analysis of ribonucleotide mixtures produced by hydrolysis of total RNA extracts from S. cerevisiae that was grown under hyperosmotic and heat shock conditions. Their global PTM profiles clearly indicated that the cellular responses to these types of stresses involved profound changes in the production of specific PTMs. The observed changes involved not only up-/down-regulation of typical PTMs, but also the outright induction of new ones that were absent under normal conditions, or the elimination of others that were normally present. Pointing toward the broad involvement of different classes of RNAs, many of the newly observed PTMs differed from those engaged in the known tRNA-based mechanism of translational recoding, which is induced by oxidative stress. Some of the expression effects were stress-specific, whereas others were not, thus suggesting that RNA PTMs may perform multifaceted activities in stress response, which are subjected to distinctive regulatory pathways. To explore their signaling networks, we implemented a strategy based on the systematic deletion of genes that connect established response genes with PTM biogenetic enzymes in a putative interactomic map. The results clearly identified PTMs that were under direct HOG control, a well-known protein kinase pathway involved in stress response in eukaryotes. Activation of this signaling pathway has been shown to result in the stabilization of numerous mRNAs and the induction of selected lncRNAs involved in chromatin remodeling. The fact that PTMs are capable of altering the activity of the parent RNAs suggest their possible participation in feedback mechanisms aimed at modulating the regulatory functions of such RNAs. This tantalizing hypothesis will be the object of future studies.

Linear ion trap with added octopole field component: the property and method

It is well known that superimposition of some positive octopole field will benefit the performance of ion trap mass analyzer. In the radial-ejection linear ion trap (LIT), adding some octopole field component to the main quadrupole field is usually accomplished by stretching the ejection rod pair. In this study, the effect of octopole potential and some other higher order potential on the performance of LIT mass analyzer is investigated. A simple and effective method, which is to add some octopole component by building a LIT with a pair of rectangular electrodes and a pair of semi-circular electrodes, is reported. Its properties were studied by numerical simulations and experiments. The results showed that a certain amount of positive octopole component could be produced by simply adjusting the position and width of the rectangular electrodes. A resolution of over 1200 at m/z 609 (~1600 Da/s) was observed in this type of LIT. They also performed tandem mass spectrometry well. The device with optimum geometry for ion ejection from rectangular electrodes provided comparable performance to that for ion ejection from semi-circular electrodes. This type of LIT design is easy for fabrication and assembly.

Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics

The elucidation of the biological significance of RNA post-transcriptional modifications is hampered by the dearth of effective high-throughput sequencing approaches for detecting, locating, and tracking their levels as a function of predetermined experimental factors. With the goal of confronting this knowledge gap, we devised a strategy for completing global surveys of all ribonucleotide modifications in a cell, which is based on the analysis of whole cell extracts by direct infusion electrospray ionization mass spectrometry (ESI-MS). Our approach eschews chromatographic separation to promote instead the direct application of MS techniques capable of providing detection, differentiation, and quantification of post-transcriptional modifications (PTMs) in complex ribonucleotide mixtures. Accurate mass analysis was used to carry out database-aided identification of PTMs, whereas multistep tandem mass spectrometry (MS(n)) and consecutive reaction monitoring (CRM) provided the necessary structural corroboration. We demonstrated that heat-map plots afforded by ion mobility spectrometry mass spectrometry (IMS-MS) can provide comprehensive modification profiles that are unique for different cell types and metabolic states. We showed that isolated tRNA samples can be used as controlled sources of PTMs in standard-additions quantification. Intrinsic internal standards enable direct comparisons of heat-maps obtained under different experimental conditions, thus offering the opportunity to evaluate the global effects of such conditions on the expression levels of all PTMs simultaneously. This type of comparative analysis will be expected to support the investigation of the system biology of RNA modifications, which will be aimed at exploring mutual correlations of their expression levels and providing new valuable insights into their biological significance.

Microsecond pulsed hydrogen/deuterium exchange of electrosprayed ubiquitin ions stored in a linear ion trap

The pulsed HDX MS method is sampling a population of ubiquitin ions with a similar backbone fold as solution.

Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics

A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

Mass spectrometric study of gas-phase ions of acid β-glucosidase (Cerezyme) and iminosugar pharmacological chaperones

The effect on the conformations and stability of gas-phase ions of Cerezyme, a glycoprotein, when bound to three small-molecule chaperones has been studied using intact ESI MS, collision cross section and MS/MS measurements. To distinguish between the peaks from apo and small-molecule complex ions, Cerezyme is deglycosylated (dg-Cer). ESI MS of dg-Cer reveals that glycosylation accounts for 8.5% of the molecular weight. When excess chaperone, either covalent (2FGF) or noncovalent (A and B iminosugars), is added to solutions of dg-Cer, mass spectra show peaks from 1:1 chaperone-enzyme complexes as well as free enzyme. On average, ions of the apoenzyme have 1.6 times higher cross sections when activated in the source region of the mass spectrometer. For a given charge state, ions of complexes of 2FGF and B have about 30% and 8.4% lower cross sections, respectively, compared to the apoenzyme. Thus, binding the chaperones causes the gas-phase protein to adopt more compact conformations. The noncovalent complex ions dissociate by the loss of charged chaperones. In the gas phase, the relative stability of dg-Cer with B is higher than that with the A, whereas in solution A binds enzyme more strongly than B. Nevertheless, the disagreement is explained based on the greater number of contacts between the B and dg-Cer than the A and dg-Cer (13 vs. 8), indicating the importance of noncovalent interactions within the protein-chaperone complex in the absence of solvent. Findings in this work suggest a hypothesis towards predicting a consistent correlation between gas-phase properties to solution binding properties.

Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition

The challenges posed by the analysis of mono-nucleotide mixtures by direct infusion electrospray ionization were examined in the context of recent advances of mass spectrometry (MS) technologies. In particular, we evaluated the merits of high-resolution mass analysis, multistep gas-phase dissociation, and ion mobility determinations for the characterization of species with very similar or identical elemental composition. The high resolving power afforded by a linear trap quadrupole-orbitrap allowed the complete differentiation of overlapping isotopic distributions produced by nucleotides that differed by a single mass unit. Resolving (12)C signals from nearly overlapped (13)C contributions provided the exact masses necessary to calculate matching elemental compositions for unambiguous formulae assignment. However, it was the ability to perform sequential steps of gas-phase dissociation (i.e. MS(n)-type analysis) that proved more valuable for discriminating between truly isobaric nucleotides, such as the AMP/dGMP and UMP/ΨMP couples, which were differentiated in the mixture from their unique fragmentation patterns. The identification of diagnostic fragments enabled the deconvolution of dissociation spectra containing the products of coexisting isobars that could not be individually isolated in the mass-selection step. Approaches based on ion mobility spectrometry-MS provided another dimension upon which isobaric nucleotides could be differentiated according to their distinctive mobility behaviors. Subtle structural variations, such as the different positions of an oxygen atom in AMP/dGMP or the glycosidic bond in UMP/ΨMP, produced detectable differences in the respective ion mobility profiles, which enabled the differentiation of the isobaric couples in the mixture. Parallel activation of all ions emerging from the ion mobility element provided an additional dimension for differentiating these analytes on the basis of both mobility and fragmentation properties.

The effect of a covalent and a noncovalent small-molecule inhibitor on the structure of Abg β-glucosidase in the gas-phase

The effects of binding two small-molecule inhibitors to Agrobacterium sp. strain ATCC 21400 (Abg) β-glucosidase on the conformations and stability of gas-phase ions of Abg have been investigated. Biotin-iminosugar conjugate (BIC) binds noncovalently to Abg while 2,4-dinitro-2-deoxy-2-fluoro-β-D-glucopyranoside (2FG-DNP) binds covalently with loss of DNP. In solution, Abg is a dimer. Mass spectra show predominantly dimer ions, provided care is taken to avoid dissociation of dimers in solution and dimer ions in the ion sampling interface. When excess inhibitor, either covalent or noncovalent, is added to solutions of Abg, mass spectra show peaks almost entirely from 2:2 inhibitor-enzyme dimer complexes. Tandem mass spectrometry experiments show similar dissociation channels for the apo-enzyme and 2FG-enzyme dimers. The +21 dimer produces +10 and +11 monomers. The internal energy required to dissociate the +21 2FG-enzyme to its monomers (767 ± 30 eV) is about 36 eV higher than that for the apo-enzyme dimer (731 ± 6 eV), reflecting the stabilization of the free enzyme dimer by the 2FG inhibitor. The primary dissociation channels for the noncovalent BIC-enzyme dimer are loss of neutral and charged BIC. The internal energy required to induce loss of BIC is 482 ± 8 eV, considerably less than that required to dissociate the dimers. For a given charge state, ions of the covalent and noncovalent complexes have about 15 % and 25 % lower cross sections, respectively, compared with the apo-enzyme. Thus, binding the inhibitors causes the gas-phase protein to adopt more compact conformations. Noncovalent binding surprisingly produces the greatest change in protein ion conformation, despite the weaker inhibitor binding. ᅟ

Investigation of non-enzymatic glycosylation of human serum albumin using ion trap-time of flight mass spectrometry

Non-enzymatic glycosylation or glycation involves covalent attachment of reducing sugar residues to proteins without enzyme participation. Glycation of glucose to human serum albumin in vivo is related to diabetes and many other diseases. We present an approach using liquid chromatography coupled to an electrospray ionization source of a hybrid ion trap-time of flight (IT-TOF-MS/MS) tandem mass spectrometer to identify the glycation sites on serum albumin from both a healthy person and a diabetic patient. The MetID software, which is commonly used for screening metabolites, is adapted for peptide fingerprinting based on both m/z values and isotopic distribution profiles. A total of 21 glycation sites from the healthy person and 16 glycation sites from the diabetic patient were identified successfully. We also demonstrate the use of matrix assisted laser desorption ionization-time of flight mass spectrometry to estimate the incorporation ratio of glucose to albumin during glycation. Results from this study show that the glycation in healthy person is more complicated than previously thought. Further analysis of incorporation ratio distribution may be necessary to accurately reflect the change of serum albumin glycation in diabetic patients.

Solution and gas-phase H/D exchange of protein-small-molecule complexes: Cex and its inhibitors

The properties of noncovalent complexes of the enzyme exo-1,4-β-D-glycanase ("Cex") with three aza-sugar inhibitors, deoxynojirimycin (X(2)DNJ), isofagomine lactam (X(2)IL), and isofagomine (X(2)IF), have been studied with solution and gas-phase hydrogen deuterium exchange (H/Dx) and measurements of collision cross sections of gas-phase ions. In solution, complexes have lower H/Dx levels than free Cex because binding the inhibitors blocks some sites from H/Dx and reduces fluctuations of the protein. In mass spectra of complexes, abundant Cex ions are seen, which mostly are formed by dissociation of complexes in the ion sampling interface. Both complex ions and Cex ions formed from a solution containing complexes have lower cross sections than Cex ions from a solution of Cex alone. This suggests the Cex ions formed by dissociation "remember" their solution conformations. For a given charge, ions of the complexes have greater gas-phase H/Dx levels than ions of Cex. Unlike cross sections, H/Dx levels of the complexes do not correlate with the relative gas-phase binding strengths measured by MS/MS. Cex ions from solutions with or without inhibitors, which have different cross sections, show the same H/Dx level after 15 s, indicating the ions may fold or unfold on the seconds time scale of the H/Dx experiment. Thus, cross sections show that complexes have more compact conformations than free protein ions on the time scale of ca. 1 ms. The gas-phase H/Dx measurements show that at least some complexes retain different conformations from the Cex ions on a time scale of seconds.

Gas-phase ions of human hemoglobin A, F, and S

Hemoglobin (Hb) (α(2)β(2)) is a tetrameric protein-protein complex. Collision cross sections, hydrogen exchange levels, and tandem mass spectrometry have been used to investigate the properties of gas-phase monomer, dimer, and tetramer ions of adult human hemoglobin (Hb A, α(2)β(2)), and two variant hemoglobins: fetal hemoglobin (Hb F, α(2)γ(2)) and sickle hemoglobin (Hb S, α(2)β(2), E6V[β]). All three proteins give similar mass spectra. Monomers of Hb S and Hb F have similar cross sections, ca. 10% greater than those of Hb A. Cross sections of dimer ions of Hb S are 11% greater than those of Hb A and 6% greater than those of Hb F. Tetramers of Hb S are 13% larger than tetramers of Hb A or Hb F. Monomers and dimers of all three Hb have similar hydrogen-deuterium exchange (HDX) levels. Tetramers of Hb S exchange 16% more hydrogens than Hb A and Hb F. In tandem mass spectrometry, monomers of Hb S and Hb F require ca. 10% greater internal energy for heme loss than Hb A. Dimers (+11) of Hb A and Hb S dissociate to monomers with asymmetrical charge division; dimers of Hb F (+11) dissociate with nearly equal charge division. Tetramer ions dissociate to monomers and trimers, unlike solution Hb, which dissociates to dimers. The most stable dimers are from Hb S; the most stable tetramers from Hb F. The results with Hb S show that a single mutation in the β chain can change the physical properties of this gas-phase protein-protein complex.

From known knowns to known unknowns: predicting in vivo drug metabolites

'It is better to be useful than perfect'. This review attempts to critically cover and assess the currently available approaches and tools to answer the crucial question: Is it possible (and if it is, to what extent is it possible) to predict in vivo metabolites and their abundances on the basis of in vitro and preclinical animal studies? In preclinical drug development, it is possible to produce metabolite patterns from a candidate drug by virtual means (i.e., in silico models), but these are not yet validated. However, they may be useful to cover the potential range of metabolites. In vitro metabolite patterns and apparent relative abundances are produced by various in vitro systems employing tissue preparations (mainly liver) and in most cases using liquid chromatography-mass spectrometry analytical techniques for tentative identification. The pattern of the metabolites produced depends on the enzyme source; the most comprehensive source of drug-metabolizing enzymes is cultured human hepatocytes, followed by liver homogenate fortified with appropriate cofactors. For specific purposes, such as the identification of metabolizing enzyme(s), recombinant enzymes can be used. Metabolite data from animal in vitro and in vivo experiments, despite known species differences, may help pinpoint metabolites that are not apparently produced in in vitro human systems, or suggest alternative experimental approaches. The range of metabolites detected provides clues regarding the enzymes attacking the molecule under study. We also discuss established approaches to identify the major enzymes. The last question, regarding reliability and robustness of metabolite extrapolations from in vitro to in vivo, both qualitatively and quantitatively, cannot be easily answered. There are a number of examples in the literature suggesting that extrapolations are generally useful, but there are only a few systematic and comprehensive studies to validate in vitro-in vivo extrapolations. In conclusion, extrapolation from preclinical metabolite data to the in vivo situation is certainly useful, but it is not known to what extent.

High-resolution excitation of ions in a low-pressure linear ion trap

An exploration of the parameters necessary to obtain high-resolution excitation, using dipolar excitation, of an ion in a linear ion trap has been undertaken in this study. These parameters included ion trap pressure, excitation amplitude, excitation period, drive frequency of the ion trap, Mathieu q value and the mass of the ion of interest. An understanding of how these parameters play a role in high-resolution excitation is necessary to the development of a method for the targeted tandem mass spectrometric (MS/MS) analysis of ions with the same nominal mass. Resonance excitation profiles with full width half maxima as narrow as 0.015 m/z units could be obtained, under the right conditions, for an ion from a homogenously substituted triazatriphosphorine at m/z 322.049, which translates into a mass resolution of >21 500. In this particular case the requirement for high resolution was a low trap pressure (3.8 × 10(-5) Torr), low excitation amplitude (3 mV), long excitation period (100 ms) and a high Mathieu q value(0.8) when using a drive frequency of 1.228 MHz. Similar conditions were used to demonstrate the isolation of individual [M + H](+) component ions from mixtures of bromazepam (m/z 316.008)/chlorprothixene (m/z 316.0921)/fendiline (m/z 316.206) and chlorprothixene (m/z 316.0921)/oxycodone (m/z 316.1543)/fendiline (m/z 316.206) prior to obtaining product ion spectra with excitation at q = 0.236. In the former mixture the individual components were isolated with near 100% efficiency while in the latter mixture the isolation efficiency dropped to near 50% for the oxycodone component and to 80% for the other components.

Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis

The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.

Gas-phase H/D exchange and collision cross sections of hemoglobin monomers, dimers, and tetramers

The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.

Conformations of gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and beta-lactoglobulin produced from two different solution conformations

At low pH in solutions of 50% methanol, proteins form expanded denatured states (the "H" state). In 90% methanol, proteins form expanded helical denatured states with artificial alpha-helices (the "H(c)" state). Gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and native and disulfide-reduced beta-lactoglobulin were formed by electrospray ionization (ESI) of the proteins from the H and H(c) states in solution. Both states in solution produce the same charge states in ESI. The conformations of the ions were studied with cross section measurements and gas-phase H/D exchange experiments. The cross sections show that the ions retain considerable folded structure. For a given protein and given charge state, ions produced from the H and H(c) states showed the same cross sections (within approximately 1%). Ions of cytochrome c, apomyoglobin, and native and reduced beta-lactoglobulin of a given charge state showed no differences in H/D exchange level when produced from the H or H(c) state. However, ubiquitin ions produced from the H(c) state consistently exchange fewer ( approximately 13%) hydrogens than ions produced from the H state, suggesting that in this case the gas-phase protein ions retain some memory of their solution conformations.

A linear ion trap mass spectrometer with versatile control and data acquisition for ion/ion reactions

A linear ion trap (LIT) with electrospray ionization (ESI) for top-down protein analysis has been constructed. An independent atmospheric sampling glow discharge ionization (ASGDI) source produces reagent ions for ion/ion reactions. The device is also meant to enable a wide variety of ion/ion reaction studies. To reduce the instrument's complexity and make it available for wide dissemination, only a few simple electronics components were custom built. The instrument functions as both a reaction vessel for gas-phase ion/ion reactions and a mass spectrometer using mass-selective axial ejection. Initial results demonstrate trapping efficiency of 70% to 90% and the ability to perform proton transfer reactions on intact protein ions, including dual polarity storage reactions, transmission mode reactions, and ion parking.

Characteristics and comparison of different radiofrequency-only multipole cooling cells

Various multipole cooling cells are widely used in mass spectrometry for their outstanding performance with regard to transmission and cooling effects. Among these, radiofrequency (RF)-only quadrupoles, hexapoles, and octopoles are routinely used in practical instrumentation. A study of their performance has been carried out using a house-built electrospray time-of-flight mass spectrometer equipped with three different multipole devices. In addition, a user-written program was developed using SIMION 7.0 to simulate ion transmission characteristics for the different devices utilized. Systematic experiments and simulations were performed with an RF-only quadrupole, hexapole, and octopole to study their theoretical and practical characteristics.

Quadrupole excitation of ions in linear quadrupole ion traps with added octopole fields

Modeling and experimental studies of quadrupole excitation of ions in linear quadrupole traps with added octopole fields are described. An approximate solution to the equations of motion of ions trapped in a quadrupole with added octopole and dodecapole fields, with quadrupole excitation and damping is given. The solutions give the steady-state or stationary amplitudes of oscillation with different excitation frequencies. Trajectory calculations of the oscillation amplitudes are also presented. The calculations show that there can be large changes in the amplitude of ion oscillation with small changes in excitation frequency, on both the low and high-frequency sides of a resonance. Results of experiments with quadrupole excitation of reserpine ions in linear quadrupole traps with 2.0%, 2.6%, and 4.0% added octopole fields are given. It is found that as the excitation frequency is changed, two resonances are generally observed, which are attributed to the motion in the x and y directions. The two resonances can have quite different intensities. Sudden jumps or sharp sided resonances are not observed, although in some cases asymmetric resonances are seen. The calculated frequency differences between the two resonances are in approximate agreement with the experiments.

Ion funnel trap interface for orthogonal time-of-flight mass spectrometry

A combined electrodynamic ion funnel and ion trap coupled to an orthogonal acceleration (oa)-time-of-flight mass spectrometer was developed and characterized. The ion trap was incorporated through the use of added terminal electrodynamic ion funnel electrodes enabling control over the axial dc gradient in the trap section. The ion trap operates efficiently at a pressure of approximately 1 Torr, and measurements indicate a maximum charge capacity of approximately 3 x 10(7) charges. An order of magnitude increase in sensitivity was observed in the analysis of low concentration peptides mixtures with orthogonal acceleration (oa)-time-of-flight mass spectrometry (oa-TOF MS) in the trapping mode as compared to the continuous regime. A signal increase in the trapping mode was accompanied by reduction in the chemical background, due to more efficient desolvation of, for example, solvent related clusters. Controlling the ion trap ejection time was found to result in efficient removal of singly charged species and improving signal-to-noise ratio (S/N) for the multiply charged analytes.

Mass analysis in islands of stability with linear quadrupoles with added octopole fields

Mass analysis with linear quadrupole mass filters is possible by forming "islands" in the stability diagram with auxiliary quadrupole excitation. In this work, computer simulations are used to calculate stability boundaries, island positions, and peak shapes and ion transmission for mass analysis with linear quadrupole mass filters that have added octopole fields of about 2 to 4%. Rod sets with exact geometries that have quadrupole and octopole fields only in the potential, and round rod sets, with multipoles up to N = 10 (the twenty pole term) included in the calculations, show the same stability boundaries, island positions, and peak shapes. With the DC voltage applied to the rods so that the Mathieu parameter a < 0, conventional mass analysis is possible without the use of an island. With the DC polarity reversed so that a > 0, the resolution and transmission are poor preventing conventional mass analysis. In principle, mass analysis in an island is possible with operation at either of two tips. Provided the correct island tip is chosen for mass analysis, peak shapes comparable to those with a > 0 and no excitation are possible, both with a > 0 and with a < 0. In the latter case, the use of an island of stability allows mass analysis when the added octopole otherwise prevents conventional mass analysis.

Study of the enhancement of dipolar resonant excitation by linear ion trap simulations

Resolution improvements in dipolar resonant excitation have been examined in a round-rod quadrupolar collision cell for values of the Mathieu characteristic exponent beta equal to n/p, where n and m are small integers (prime beta values) versus other beta values where n and p are not small (ordinary beta values). The trajectories of ions moving in the time-varying electric fields of a quadrupole with and without buffer-gas molecules were calculated to determine the relationship of prime and ordinary beta values to frequency resolution for resonant ion excitation and ejection. For prime beta values, the ion trajectory in the hyperbolic quadrupole field will be exactly periodic with a period of at most 4 pi p/Omega, where Omega is the angular frequency of the main drive radio-frequency (RF) potential. Ion trajectory simulations with prime beta versus ordinary beta values show that the motion of ions with prime beta values have simpler trajectories of shorter periods. Frequency response profiles (FRPs) for round-rod quadrupoles at zero pressure show that dipolar resonant excitations with prime beta values exhibit significantly narrower bandwidths than those with ordinary beta values. Simulations show that at 0.05 to 0.8 mTorr of nitrogen, it is possible to reduce the FRP bandwidth by 20% (measured at 50% depth).

Rapid separation and identification of phenolic and diterpenoid constituents from Radix Salvia miltiorrhizae by high-performance liquid chromatography diode-array detection, electrospray ionization time-of-flight mass spectrometry and electrospray ionization quadrupole ion trap mass spectrometry

High-performance liquid chromatography-diode array detection (HPLC-DAD), electrospray ionization time-of-flight mass spectrometry (HPLC-ESI-TOF-MS) and electrospray ionization quadrupole ion trap mass spectrometry (HPLC-ESI-MSn) were used for the isolation, identification and structural analysis of water-soluble phenolic and nonpolar diterpenoid constituents in Dan-shen (Radix Salvia miltiorrhizae) which was prepared by sonication in 70% methanol. Mass spectra were obtained by ESI-TOF-MS and electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT-MS). A formula database of known constituents in Dan-shen was established and most constituents were rapidly identified by HPLC-DAD/ESI-TOF-MS by matching their accurate molecular masses with the formulae of the compounds in the database. Compounds with the same molecular formula could not be differentiated by TOF-MS; however, QIT-MS could differentiate those compounds and elucidate their structures based on their characteristic fragmentation. HPLC-DAD, HPLC/ESI-TOF-MS and HPLC/ESI-MSn provided complementary information for the identification of the constituents in Dan-shen. Forty constituents were identified in 30 min based on their positive and negative ion ESI mass spectra and liquid chromatographic information. Thus the method described is useful for the rapid analysis of multiple constituents in Dan-shen.

Ion trap collision-induced dissociation of human hemoglobin alpha-chain cations

Multiply protonated human hemoglobin alpha-chain species, ranging from [M + 4H]4+ to [M + 20H]20+, have been subjected to ion trap collisional activation. Cleavages at 88 of the 140 peptide bonds were indicated, summed over all charge states, although most product ion signals were concentrated in a significantly smaller number of channels. Consistent with previous whole protein ion dissociation studies conducted under similar conditions, the structural information inherent to a given precursor ion was highly sensitive to charge state. A strongly dominant cleavage at D75/M76, also noted previously in beam-type collisional activation studies, was observed for the [M + 8H]8+ to [M + 11H]11+ precursor ions. At lower charge states, C-terminal aspartic acid cleavages were also prominent but the most abundant products did not arise from the D75/M76 channel. The [M + 12H]12+-[M + 16H]16+ precursor ions generally yielded the greatest variety of amide bond cleavages. With the exception of the [M + 4H]4+ ion, all charge states showed cleavage at the L113/P114 bond. This cleavage proved to be the most prominent dissociation for charge states [M + 14H]14+ and higher. The diversity of dissociation channels observed within the charge state range studied potentially provides the opportunity to localize residues associated with variants via a top-down tandem mass spectrometry approach.

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.

Cyclic polyamide oligomers extracted from nylon 66 membrane filter disks as a source of contamination in liquid chromatography/mass spectrometry

Background interferences are perhaps an unavoidable part of analytical detection schemes, particularly when analyzing trace level samples or when using detectors with high levels of sensitivity. In liquid chromatography, mobile phase solvents are routinely filtered using membrane filter disks to trap particulates in hopes of minimizing contamination, providing improvements in data output and instrumental operation. In this study, we report that one such filter disk leads to a significant level of contamination in LC and LC/MS experiments. Extractable compounds from nylon membrane filters generate significant background signals in UV absorption chromatograms at 214 nm, and are also detected by electrospray ionization mass spectrometry, with nominal m/z values of 453 and 679. It is shown that rinsing the nylon membranes before their use can reduce, but will not eliminate, the extractable contaminants from the mobile phase. Through MS and tandem MS analysis, we have identified these contaminants as cyclic oligomers of polyamide 66. Based on these results, it is recommended that nylon membrane filters be avoided when conducting trace level analysis, particularly when conducting LC/MS experiments.

Feasibility of different mass spectrometric techniques and programs for automated metabolite profiling of tramadol in human urine

The purpose of the study was to determine the advantages of different mass spectrometric instruments and commercially available metabolite identification programs for metabolite profiling. Metabolism of tramadol hydrochloride and the excretion of it and its metabolites into human urine were used as a test case because the metabolism of tramadol is extensive and well known. Accurate mass measurements were carried out with a quadrupole time-of-flight mass spectrometer (Q-TOF) equipped with a LockSpray dual-electrospray ionization source. A triple quadrupole mass spectrometer (QqQ) was applied for full scan, product ion scan, precursor ion scan and neutral loss scan measurements and an ion trap instrument for full scan and product ion measurements. The performance of two metabolite identification programs was tested. The results showed that metabolite programs are time-saving tools but not yet capable of fully automated metabolite profiling. Detection of non-expected metabolites, especially at low concentrations in a complex matrix, is still almost impossible. With low-resolution instruments urine samples proved to be challenging even in a search for expected metabolites. Many false-positive hits were obtained with the automated searching and manual evaluation of the resulting data was required. False positives were avoided by using the higher mass accuracy Q-TOF. Automated programs were useful for constructing product ion methods, but the time-consuming interpretation of mass spectra was done manually. High-quality MS/MS spectra acquired on the QqQ instrument were used for confirmation of the tramadol metabolites. Although the ion trap instrument is of undisputable benefit in MS(n), the low mass cutoff of the ion trap made the identification of tramadol metabolites difficult. Some previously unreported metabolites of tramadol were found in the tramadol urine sample, and their identification was based solely on LC/MS and LC/MS/MS measurements.

‘Top-down’ characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trap

The gas-phase fragmentation reactions of a series of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase have been examined by multistage tandem mass spectrometry (MS/MS and MS(3)) in a linear quadrupole ion trap in order to explore the utility of this instrumentation for routine 'top-down' recombinant protein characterization. Following a rapid low resolution survey of the fragmentation behavior of the precursor ions from the wild type (WT) protein, selected charge states were subjected to detailed structural characterization by using high resolution 'zoom' and 'ultrazoom' resonance ejection MS/MS product ion scans. Dissociation of the [M + 18H](18+) charge state yielded a range of product ions from which extensive sequence information could be derived. In contrast, dissociation of the [M + 20H](20+) charge state resulted in a single dominant y(96) product ion formed by fragmentation between adjacent Ile/Gly residues, with only limited sequence coverage. Further extensive sequence information was readily obtained however, by MS(3) dissociation of this initial product. From the combined MS/MS and MS(3) spectra an overall sequence coverage of 66.9%, with fragmentation of 85 of the 127 amide bonds within the WT protein, was obtained. MS/MS and MS(3) of three of the four site-directed mutagenesis products (E29A), (Y61F) and (E81A) were found to yield essentially identical product ion spectra to the WT protein, indicating that these modifications had no significant influence on the fragmentation behavior. The specific site of modification could be unambiguously determined in each case by characterization of product ions resulting from fragmentation of amide bonds on either side of the mutation site. In contrast, MS/MS and MS(3) of the K107A mutant led to significantly different product ion spectra dominated by cleavages occurring N-terminal to proline, which restricted the ability to localize the modification site to within only an 8 amino acid region of the sequence. This work highlights the need for further studies to characterize the charge state, sequence and structural dependence to the low energy collision induced dissociation reactions of multiply protonated intact protein ions.

Recent advances in the application of capillary electrophoresis with mass spectrometric detection

This review gives an overview of applications of CE coupled to MS detection published in the literature of the last three years. The works discussed in this paper comprise a wide range of different fields of application. These include important sections such as the analysis of biomolecules, the analysis of pharmaceuticals and their metabolites in different matrices, environmental analysis, and also investigations on the composition of technical products.

Selective detection and identification of phosphopeptides by dansyl MS/MS/MS fragmentation

Protein phosphorylation regulates many cellular processes and pathways, such as cell cycle progression, signal transduction cascades and gene expression. Selective detection of phosphopeptides from proteolytic digests is a challenging and highly relevant task in many proteomics applications. Often phosphopeptides are present in small amounts and need selective isolation or enrichment before identification. Here we report a novel approach to label selectively phospho-Ser/-Thr residues by exploiting the features of a novel linear ion trap mass spectrometer. Using dansyl labelling and MS3 fragmentation, we developed a method useful for the large-scale proteomic profiling of phosphorylation sites. The new residues in the sequence were stable and easily identifiable under general conditions for tandem mass spectrometric sequencing.

Ion excitation in a linear quadrupole ion trap with an added octopole field

Modeling of ion motion and experimental investigations of ion excitation in a linear quadrupole trap with a 4% added octopole field are described. The results are compared with those obtained with a conventional round rod set. Motion in the effective potential of the rod set can explain many of the observed phenomena. The frequencies of ion oscillation in the x and y directions shift with amplitude in opposite directions as the amplitudes of oscillation increase. Excitation profiles for ion fragmentation become asymmetric and in some cases show bistable behavior where the amplitude of oscillation suddenly jumps between high and low values with very small changes in excitation frequency. Experiments show these effects. Ions are injected into a linear trap, stored, isolated, excited for MS/MS, and then mass analyzed in a time-of-flight mass analyzer. Frequency shifts between the x and y motions are observed, and in some cases asymmetric excitation profiles and bistable behavior are observed. Higher MS/MS efficiencies are expected when an octopole field is added. MS/MS efficiencies (N(2) collision gas) have been measured for a conventional quadrupole rod set and a linear ion trap with a 4% added octopole field. Efficiencies are chemical compound dependent, but when an octopole field is added, efficiencies can be substantially higher than with a conventional rod set, particularly at pressures of 1.4 x 10(-4) torr or less.