Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface

Genetic Algorithm Optimized Printed Circuit Board Ion Funnel Tandem Subambient Pressure Ionization with Nanoelectrospray (SPIN) for High Sensitivity Mass Spectrometry

The SPIN tandem ion funnel (IF) structure allows for highly sensitive mass spectrometry due to reduced ion losses in the interface region and during transmission; however, IF has an inherent mass discrimination problem, which can greatly restrain the ion transmission efficiency (TE) and therefore requires certain optimization methods. Conventional optimization methods ignore the combined effects of multiple IF characteristic parameters (electrical and dimensional parameters) and are unable to achieve efficient ion transmission over a wide mass range, thus requiring significant tuning time. In this paper, a genetic algorithm (GA)-optimized printed circuit board ion funnel (PCBIF) was designed, fabricated, preliminarily evaluated, and integrated into the SPIN interface to address the ion loss that can occur when mass spectrometers transfer ions at subambient pressure. Simulation studies have showed clearly that the effective automated GA can increase the PCBIF optimization, design, and the ion TE (finding the optimal characteristic parameters within 4 h and achieving 96% ion TE for ions with m/z between 50 and 700). Preliminary tests on built SPIN-PCBIF-MS can lead to an LOD of 0.01 nM and also indirectly suggest the effectiveness of the GA-optimized PCBIF. The proposed GA method helps to guide the design of IF and can also be used for other multivariate mass analyzers or ion transmission devices.

Implementation of Ion Mobility Spectrometry-Based Separations in Structures for Lossless Ion Manipulations (SLIM)

Structures for Lossless Ion Manipulations (SLIM) is a powerful variant of traveling wave ion mobility spectrometry (TW-IMS) that uses a serpentine pattern of microelectrodes deposited onto printed circuit boards to achieve ultralong ion path lengths (13.5 m). Ions are propelled through SLIM platforms via arrays of TW electrodes while RF and DC electrodes provide radial confinement, establishing near lossless transmission. The recent ability to cycle ions multiple times through a SLIM has allowed ion path lengths to exceed 1000 m, providing unprecedented separation power and the ability to observe ion structural conformations unobtainable with other IMS technologies. The combination of high separation power, high signal intensity, and the ability to couple with mass spectrometry places SLIM in the unique position of being able to address longstanding proteomics and metabolomics challenges by allowing the characterization of isomeric mixtures containing low abundance analytes.

Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter

Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it greatly affects signal-to-noise ratio and MS resolution measurements. Here, we report on the integration of a 2 GS/s, 14-bit ADC with structures for lossless ion manipulations (SLIM-IMS-MS) and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided a reduction in the digitized noise by a factor of ∼6, owing largely to the use of smaller bit sizes. The low baseline allowed threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a mixture of heavy labeled phosphopeptides showed that the 14-bit ADC provided a ∼1.5-2× signal-to-noise (S/N) increase for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernible signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ∼14-fold fewer mass spectra to be averaged to produce a mass spectrum with a similar S/N as the 8-bit ADC, demonstrating ∼10× higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra and provides a much better picture of analyte profiles in complex mixtures.

Design and Performance of a Soft-Landing Instrument for Fragment Ion Deposition

We report the development of a new high-flux electrospray ionization-based instrument for soft landing of mass-selected fragment ions onto surfaces. Collision-induced dissociation is performed in a collision cell positioned after the dual electrodynamic ion funnel assembly. The high duty cycle of the instrument enables high-coverage deposition of mass-selected fragment ions onto surfaces at a defined kinetic energy. This capability facilitates the investigation of the reactivity of gaseous fragment ions in the condensed phase. We demonstrate that the observed reactions of deposited fragment ions are dependent on the structure of the ion and the composition of either ionic or neutral species codeposited onto a surface. The newly developed instrument provides access to high-purity ion fragments as building blocks for the preparation of unique ionic layers.

Characterization of Electrospray Drop Size Distributions by Mobility-Classified Mass Spectrometry: Implications for Ion Clustering in Solution and Ion Formation Pathways

One of the outcomes of electrospray ionization is the size distribution of the droplets, which determines, together with the solvent composition and the source gas temperature, the minimum distance from the sprayer tip to the mass spectrometer inlet and therefore the ion transfer efficiency. Even more importantly, the average number of analyte molecules and, if present, contaminant species per droplet depend on the drop size. Consequently, the drop size distribution is a key parameter in nonspecific ion clustering in solution and ion suppression. The finding that small droplet sizes improve the mass spectral quality led to the development of nanoelectrospray sources, which dispense liquid flow rates below 0.1 μL/min and can generate drops with diameters smaller than 100 nm. However, current discussions on the effect of drop size on ion formation pathways and efficiencies remain qualitative because the exact drop size distributions are unknown. Here, we show that ion mobility-classified mass spectrometry of raffinose cluster ions allows us to determine very precisely the drop size distribution generated by the electrospray source in positive- and negative-ion modes. Based on the derived drop size distributions, we can quantitatively predict nonspecific ion clustering and can extract accurate probabilities for emission of species from parent drops upon Coulomb fission.

Multiplexing of Electrospray Ionization Sources Using Orthogonal Injection into an Electrodynamic Ion Funnel

In this contribution, we report an efficient approach to multiplex electrospray ionization (ESI) sources for applications in analytical and preparative mass spectrometry. This is achieved using up to four orthogonal injection inlets implemented on the opposite sides of an electrodynamic ion funnel interface. We demonstrate that both the total ion current transmitted through the mass spectrometer and the signal-to-noise ratio increase by 3.8-fold using four inlets compared to one inlet. The performance of the new multiplexing approach was examined using different classes of analytes covering a broad range of mass and ionic charge. A deposition rate of >10 μg of mass-selected ions per day may be achieved by using the multiplexed sources coupled to preparative mass spectrometry. The almost proportional increase in the ion current with the number of ESI inlets observed experimentally is confirmed using gas flow and ion trajectory simulations. The simulations demonstrate a pronounced effect of gas dynamics on the ion trajectories in the ion funnel, indicating that the efficiency of multiplexing strongly depends on gas velocity field. The study presented herein opens up exciting opportunities for the development of bright ion sources, which will advance both analytical and preparative mass spectrometry applications.

Sampling Efficiency Improvement to an Electrospray Ionization Mass Spectrometer and Its Implications for Liquid Chromatography Based Inlet Systems in the Nanoliter to Milliliter per Minute Flow Range

This paper describes electrospray sampling efficiency measurements obtained on a triple quadrupole mass spectrometer equipped with a large atmosphere to vacuum sampling aperture and modified ion optics designed to confine the ions traveling in the intense expanding gas beam and prevent scattering losses in the entrance optics of the mass analyzer. Sampling efficiency, defined as the ratio of the number of ions captured in the first vacuum stage of the entrance optics to the number of analyte molecules entering the ion source, is a measure of sensitivity that takes into account both ionization efficiency at atmospheric pressure, the efficiency of transporting the ions from atmosphere to vacuum, and the efficiency of confining them in the subsequent gas expansion before mass analysis. Sampling efficiency measurements were conducted under high-performance liquid chromatography sample introduction conditions using columns and flow rates spanning the nanoflow (300 nL/min), microflow (3-60 μL/min), and milliflow (100-500 μL/min) ranges. The results show a convergence in the sampling efficiencies across this range, narrowing the sensitivity gap between the nanoflow and higher flow rate ranges largely because nanoflow sampling efficiency has been shown to be close to 100% for more than a decade, leaving little room for improvement. Under situations where sample volumes are not limiting, lower concentration detection limits can now be achieved with the higher flow rate systems versus nanoflow as a direct consequence of the higher sample loading capacity of the columns and the reduction in the difference in their ion sampling efficiencies.

Quantitative mass spectrometry imaging of drugs and metabolites: a multiplatform comparison

Mass spectrometry imaging (MSI) provides insight into the molecular distribution of a broad range of compounds and, therefore, is frequently applied in the pharmaceutical industry. Pharmacokinetic and toxicological studies deploy MSI to localize potential drugs and their metabolites in biological tissues but currently require other analytical tools to quantify these pharmaceutical compounds in the same tissues. Quantitative mass spectrometry imaging (Q-MSI) is a field with challenges due to the high biological variability in samples combined with the limited sample cleanup and separation strategies available prior to MSI. In consequence, more selectivity in MSI instruments is required. This can be provided by multiple reaction monitoring (MRM) which uses specific precursor ion-product ion transitions. This targeted approach is in particular suitable for pharmaceutical compounds because their molecular identity is known prior to analysis. In this work, we compared different analytical platforms to assess the performance of MRM detection compared to other MS instruments/MS modes used in a Q-MSI workflow for two drug candidates (A and B). Limit of detection (LOD), linearity, and precision and accuracy of high and low quality control (QC) samples were compared between MS instruments/modes. MRM mode on a triple quadrupole mass spectrometer (QqQ) provided the best overall performance with the following results for compounds A and B: LOD 35.5 and 2.5 μg/g tissue, R² 0.97 and 0.98 linearity, relative standard deviation QC <13.6%, and 97-112% accuracy. Other MS modes resulted in LOD 6.7-569.4 and 2.6-119.1 μg/g tissue, R² 0.86-0.98 and 0.86-0.98 linearity, relative standard deviation QC < 19.4 and < 37.5%, and 70-356% and 64-398% accuracy for drug candidates A and B, respectively. In addition, we propose an optimized 3D printed mimetic tissue model to increase the overall analytical throughput of our approach for large animal studies. The MRM imaging platform was applied as proof-of-principle for quantitative detection of drug candidates A and B in four dog livers and compared to LC-MS. The Q-MSI concentrations differed <3.5 times with the concentrations observed by LC-MS. Our presented MRM-based Q-MSI approach provides a more selective and high-throughput analytical platform due to MRM specificity combined with an optimized 3D printed mimetic tissue model.

Investigation by simulation of the RF carpets for the transport of ions at atmospheric pressures

Ion funnels, quadrupole, and multipole are well-known ion optic methods for transportation of ions. However, the methods are suitable for pressures below 30-40 Torr. The main loss of ions occurs in an inlet of mass spectrometer at atmospheric pressure. This work offers a focusing system, which employs a fine-structure electrode ion carpet. The focusing efficiency of fine-structure electrode was investigated by computer simulation methods and it was compared with theoretical estimation. The methods demonstrated good agreement with each other that promises a reliability of results. The authors found an optimal fine-structure electrode ion carpet configuration (electrodes width of 10 µm), which demonstrates suitable focusing efficiency and can be implemented in practice.

Numerical Simulation of Flow Field and Ion Transport for Different Ion Source Sampling Interfaces of a Mass Spectrometer

Understanding ion transport mechanisms in the flow expansion section of the first vacuum region of a mass spectrometer (MS) with an atmospheric pressure ionization source is essential for optimizing the MS sampling interface design. In this study, numerical simulations of three types of ions in two different MS interface designs have been carried out. In contrast to previously reported numerical studies, nonequilibrium gas dynamics due to rarefied gas effects has been considered in modeling the flow expansion and a realistic space charge effect has been considered in a continuous ion injection mode. Numerical simulations reveal that a flat plate interface has a higher peak buffer gas velocity but a narrower zone of silence compared to the conical interface. Shock wave structures are clearly captured, and the Knudsen number distribution is displayed. Simulation results show that in the axial direction the buffer gas effect is much stronger than the electric force effect in the current configuration. The conical interface leads to both a strong ion acceleration in the zone of silence and a strong ion deceleration downstream. In the radial direction, both the electric force and buffer gas drag force play an important role. The conical interface introduces a relatively stronger ion focusing effect from the radial buffer gas effect and a stronger ion dispersion from the radial electric force than the flat plate interface. The net effect for the current configuration is an increase in ion losses for the conical interface. Nanoelectrospray ionization experiments were carried out to validate the ion transmission efficiency.

A Simple Printed Circuit Board-Based Ion Funnel for Focusing Low m/z Ratio Ions with High Kinetic Energies at Elevated Pressure

Ion funnels are one of the key components for transferring ions from higher pressure into the vacuum. Typically, ion funnels are constructed of several different plate ring electrodes with a decreasing inner diameter where radio frequency (RF) voltages and electric DC fields are applied to the electrodes to focus and transport ion clouds. In this work, we developed and investigated a simple and low-cost ion funnel design that is based on standard printed circuit boards (PCB) with integrated planar electrodes including the signal distribution network. This ion funnel is capable of withstanding high electric fields with superimposed RF voltages due to its buried capacitors. To evaluate the ion focusing efficiency of the ion funnel, we simulated the movement of ions inside this funnel and experimentally evaluated the ion transfer. Our simulations show that a rectangular ion funnel like the PCB ion funnel has similar performance compared with conventional stacked ring funnels. Due to the hundredfold lower parasitic capacitance between the planar electrodes compared with conventional ion funnels, high RF voltage amplitudes up to 195 V and reduced electric DC field strengths up to 100 Td can be reached at a frequency of about 5 MHz. Thus, the funnel is appropriate to focus light ions at elevated pressures up to 20 mbar. Graphical Abstract .

Chemometrics-assisted optimization of liquid chromatography-quadrupole-time-of-flight mass spectrometry analysis for targeted metabolomics

Mass spectrometry-based metabolomics is characterized by a vast number of variables leading to a great degree of complexity. In this work, we aimed to simplify this process with a stepped chemometric optimization of the both funnel technology (funnel exit DC, FDC; funnel RF LP, FLC; funnel RF HP, FRP) and ion source parameters (Octopolo, Oct; and Fragmentor, Frag) of a quadrupole-time of flight (qTOF) for a human urinary metabolites. The workflow comprised a Box-Behnken experimental design with 47 experiments followed by the identification and quantification of a set of metabolites using high-resolution full-scan MS mode and feature extraction with an inclusion list. Metabolite peak areas were grouped according to abundance (high and low) and modeled by Random Forest regression (variance explained >85%). The full three-level factorial design consisting in 243 experiments was predicted and top 10 solutions for desirability function and those comprising the Pareto front were extracted and investigated. To guarantee the quality of results, we compared the Pareto front solutions with those achieved by standard instrumental parameters suggested by the manufacturer. A set of five solutions were identified that increased the mean peak area by 56-59% and 17%, for high- and low-abundance metabolites, respectively. The optimal parameters were determined to be: FLP, 100 V; FDC, 40 and 30 V; Frag, 275 and 400 V; and Oct, 600 and 800 V. The methodology applied throughout this work represents a flexible strategy to optimize instrumental parameters and exploit the performance of a qTOF MS detector.

Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation

Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.

Enhanced Ion Transmission Efficiency up to m/ z 24 000 for MALDI Protein Imaging Mass Spectrometry

The molecular identification of species of interest is an important part of an imaging mass spectrometry (IMS) experiment. The high resolution accurate mass capabilities of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) have recently been shown to facilitate the identification of proteins in matrix-assisted laser desorption/ionization (MALDI) IMS. However, these experiments are typically limited to proteins giving rise to ions of relatively low m/ z due to difficulties transmitting and measuring large molecular weight ions of low charge states. Herein we have modified the source gas manifold of a commercial MALDI FT-ICR MS to regulate the gas flow and pressure to maximize the transmission of large m/ z protein ions through the ion funnel region of the instrument. By minimizing the contribution of off-axis gas disruption to ion focusing and maximizing the effective potential wall confining the ions through pressure optimization, the signal-to-noise ratios (S/N) of most protein species were improved by roughly 1 order of magnitude compared to normal source conditions. These modifications enabled the detection of protein standards up to m/ z 24 000 and the detection of proteins from tissue up to m/ z 22 000 with good S/N, roughly doubling the mass range for which high quality protein ion images from rat brain and kidney tissue could be produced. Due to the long time-domain transients (>4 s) required to isotopically resolve high m/ z proteins, we have used these data as part of an FT-ICR IMS-microscopy data-driven image fusion workflow to produce estimated protein images with both high mass and high spatial resolutions.

Conformational Landscapes of Ubiquitin, Cytochrome c, and Myoglobin: Uniform Field Ion Mobility Measurements in Helium and Nitrogen Drift Gas

In this study, a commercial uniform field drift tube ion mobility-mass spectrometer (IM-MS) was utilized to measure the gas-phase conformational populations of three well-studied proteins: ubiquitin (8566 Da), cytochrome c (12,359 Da), and myoglobin in both apo and holo forms (16,951 and 17,567 Da, respectively) in order to evaluate the use of this technology for broadscale structural proteomics applications. Proteins were electrosprayed from either acidic organic (pH ~3) or aqueous buffered (pH ~6.6) solution phase conditions, which generated a wide range of cation charge states corresponding to both extended (unfolded) and compact (folded) gas-phase conformational populations. Corresponding collision cross section (CCS) measurements were compiled for significant ion mobility peak features observed at each charge state in order to map the conformational landscapes of these proteins in both helium and nitrogen drift gases. It was observed that the conformational landscapes were similar in both drift gases, with differences being attributed primarily to ion heating during helium operation due to the necessity of operating the instrument with higher pressure differentials. Higher resolving powers were observed in nitrogen, which allowed for slightly better structural resolution of closely-spaced conformer populations. The instrumentation was found to be particularly adept at measuring low abundance conformers which are only present under gentle conditions which minimize ion heating. This work represents the single largest ion mobility CCS survey published to date for these three proteins with 266 CCS values and 117 ion mobility spectra, many of which have not been previously reported.

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements

Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (^DTCCS_N2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these ^DTCCS_N2 values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field ^DTCCS_N2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.

New frontiers for mass spectrometry based upon structures for lossless ion manipulations

Structures for lossless ion manipulations (SLIM) provide a new paradigm for efficient, complex and extended gas phase ion manipulations. SLIM are created from electric fields generated by the application of DC and RF potentials to arrays of electrodes patterned on two parallel surfaces. The electric fields provide lossless ion manipulations, including effective ion transport and storage. SLIM modules have been developed using both constant and oscillatory electric fields (e.g. traveling waves) to affect the ion motion. Ion manipulations demonstrated to date with SLIM include: extended trapping, ion selection, ion dissociation, and ion mobility spectrometry (IMS) separations achieving unprecedented ultra high resolution. SLIM thus provide the basis for previously impractical manipulations, such as very long path length ion mobility separations where ions traverse a serpentine path multiple times, as well as new capabilities that extend the utility of these developments based on temporal and spatial compression of ion mobility separations and other ion distributions. The evolution of SLIM devices developed over the last three years is reviewed and we provide examples of various ion manipulations performed, and briefly discuss potential applications and new directions.

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules, such as proteins and lipids, and alter their properties and functions, so glycan characterization is essential for understanding the effects they have on cellular systems. However, the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycan standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest that specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS. Graphical abstract Glycan isomers, such as fructose and glucose, show distinct separations in positive and negative ion mode.

Study on diffusion behavior of analyte in an electrospray ionization source

RATIONALE

Diffusion of an analyte is one of the main determinants of reduced sensitivity in an electrospray ionization (ESI) source. In this work, the relative responses of compounds and their stable isotope-labeled (SIL) products in different injection modes were compared to investigate the diffusion behavior of analytes in ESI, without influence of other factors.

METHODS

Chloramphenicol (CAP) and D5 -CAP as well as melamine (Mel) and (13) C3 -Mel were used to illustrate the diffusion behavior in different operation modes and different ion sources, by comparing their relative responses in infusion mode and flow injection analysis (FIA) mode under variable temperature.

RESULTS

In infusion mode, sample solution was introduced by syringe, and formed a stable and continuous signal. While in FIA mode, because of the huge difference in volume between the sample solution and the mobile phase, it is assumed that analyte ionizes and transmits in the gaseous phase created by the mobile phase. Analytes formed different concentration distributions in the two injection modes. The relative responses of CAP and D5 -CAP increased from 0.81 to 0.98 when the temperature was increased from 300 °C to 650 °C in infusion mode and decreased from 1.37 to 1.17 with increasing temperature in FIA mode. The opposite trends of the two injection modes were also obtained in positive operation modes and ion sources with different configuration.

CONCLUSIONS

Opposite variation tendencies of relative responses of model samples and their stable isotope-labeled products with temperature were observed for infusion and FIA injection modes, indicating different diffusion behaviors in the two injection modes. These results provide a theoretical basis for ion source designing and better understanding of the ESI mechanism. Copyright © 2016 John Wiley & Sons, Ltd.

Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry

A novel concept for ion spatial peak compression is described, and discussed primarily in the context of ion mobility spectrometry (IMS). Using theoretical and numerical methods, the effects of using non-constant (e.g., linearly varying) electric fields on ion distributions (e.g., an ion mobility peak) is evaluated both in the physical and temporal domains. The application of a linearly decreasing electric field in conjunction with conventional drift field arrangements is shown to lead to a reduction in IMS physical peak width. When multiple ion packets (i.e., peaks) in a selected mobility window are simultaneously subjected to such fields, there is ion packet compression (i.e., a reduction in peak widths for all species). This peak compression occurs with only a modest reduction of resolution, which can be quickly recovered as ions drift in a constant field after the compression event. Compression also yields a significant increase in peak intensities. Ion mobility peak compression can be particularly useful for mitigating diffusion-driven peak broadening over very long path length separations (e.g., in cyclic multi-pass arrangements), and for achieving higher S/N and IMS resolution over a selected mobility range. Graphical Abstract ᅟ.

Design and performance evaluation of a novel ion funnel driven by a phase-modulated rectangular wave

RATIONALE

The ion funnel has proven to be an important ion transport device. It is used in mass spectrometry as a replacement for the ion transmission limited skimmer. However, conventional out-of-phase radiofrequency (RF) supply approaches inevitably produce potential barriers, decreasing transmission efficiency. A novel RF supply method is proposed that produces better transmission performance.

METHODS

We designed an ion funnel driven by a phase-modulated rectangular wave (PMRW). The potential field distributions of the PMRW ion funnel and a conventional ion funnel were computer simulated to evaluate their focusing properties. A series of simulations were produced using the SIMION ion-optics simulation program to compare the transmission efficiency of the two types of funnel. Preliminary experimental results were obtained using an electrospray ionization mass spectrometry platform with polypropylene glycol, propylamine and butylamine samples.

RESULTS

The electrical potential distribution of a PMRW ion funnel has a bowl shape at the cross section of the electrodes, rather than in the field-free region; this benefits focusing performance. A comparison of ion trajectories and flight time data produced by the SIMION simulations showed that the potential barrier did not exist in the PMRW mode. The experimental results showed that the PMRW method increased the signal intensity by 150-200% for propylamine and butylamine and 50% for polypropylene glycol.

CONCLUSIONS

A novel PMRW ion funnel has been designed and developed. The simulation and experimental results indicate that the PMRW ion funnel has better transmission efficiency than the conventional ion funnel, particularly for low mass-to-charge ratio ions.

Ion transfer from an atmospheric pressure ion funnel into a mass spectrometer with different interface options: Simulation-based optimization of ion transmission efficiency

RATIONALE

We optimized an atmospheric pressure ion funnel (APIF) including different interface options (pinhole, capillary, and nozzle) regarding a maximal ion transmission. Previous computer simulations consider the ion funnel itself and do not include the geometry of the following components which can considerably influence the ion transmission into the vacuum stage.

METHODS

Initially, a three-dimensional computer-aided design (CAD) model of our setup was created using Autodesk Inventor. This model was imported to the Autodesk Simulation CFD program where the computational fluid dynamics (CFD) were calculated. The flow field was transferred to SIMION 8.1. Investigations of ion trajectories were carried out using the SDS (statistical diffusion simulation) tool of SIMION, which allowed us to evaluate the flow regime, pressure, and temperature values that we obtained.

RESULTS

The simulation-based optimization of different interfaces between an atmospheric pressure ion funnel and the first vacuum stage of a mass spectrometer require the consideration of fluid dynamics. The use of a Venturi nozzle ensures the highest level of transmission efficiency in comparison to capillaries or pinholes. However, the application of radiofrequency (RF) voltage and an appropriate direct current (DC) field leads to process optimization and maximum ion transfer. The nozzle does not hinder the transfer of small ions.

CONCLUSIONS

Our high-resolution SIMION model (0.01 mm grid unit(-1) ) under consideration of fluid dynamics is generally suitable for predicting the ion transmission through an atmospheric-vacuum system for mass spectrometry and enables the optimization of operational parameters. A Venturi nozzle inserted between the ion funnel and the mass spectrometer permits maximal ion transmission. Copyright © 2015 John Wiley & Sons, Ltd.

Ion mobility mass spectrometry of peptide, protein, and protein complex ions using a radio-frequency confining drift cell

A new drift cell was used to measure collision cross sections and characterize the origins of ion mobility peak broadening for biological molecules and assemblies.

Developments in FTICR-MS and Its Potential for Body Fluid Signatures

Fourier transform mass spectrometry (FTMS) is the method of choice for measurements that require ultra-high resolution. The establishment of Fourier transform ion cyclotron resonance (FTICR) MS, the availability of biomolecular ionization techniques and the introduction of the Orbitrap™ mass spectrometer have widened the number of FTMS-applications enormously. One recent example involves clinical proteomics using FTICR-MS to discover and validate protein biomarker signatures in body fluids such as serum or plasma. These biological samples are highly complex in terms of the type and number of components, their concentration range, and the structural identity of each species, and thus require extensive sample cleanup and chromatographic separation procedures. Clearly, such an elaborate and multi-step sample preparation process hampers high-throughput analysis of large clinical cohorts. A final MS read-out at ultra-high resolution enables the analysis of a more complex sample and can thus simplify upfront fractionations. To this end, FTICR-MS offers superior ultra-high resolving power with accurate and precise mass-to-charge ratio (m/z) measurement of a high number of peptides and small proteins (up to 20 kDa) at isotopic resolution over a wide mass range, and furthermore includes a wide variety of fragmentation strategies to characterize protein sequence and structure, including post-translational modifications (PTMs). In our laboratory, we have successfully applied FTICR “next-generation” peptide profiles with the purpose of cancer disease classifications. Here we will review a number of developments and innovations in FTICR-MS that have resulted in robust and routine procedures aiming for ultra-high resolution signatures of clinical samples, exemplified with state-of-the-art examples for serum and saliva.

Quantitative Mass Spectrometry Reveals that Intact Histone H1 Phosphorylations are Variant Specific and Exhibit Single Molecule Hierarchical Dependence

Breast cancer was the second leading cause of cancer related mortality for females in 2014. Recent studies suggest histone H1 phosphorylation may be useful as a clinical biomarker of breast and other cancers because of its ability to recognize proliferative cell populations. Although monitoring a single phosphorylated H1 residue is adequate to stratify high-grade breast tumors, expanding our knowledge of how H1 is phosphorylated through the cell cycle is paramount to understanding its role in carcinogenesis. H1 analysis by bottom-up MS is challenging because of the presence of highly homologous sequence variants expressed by most cells. These highly basic proteins are difficult to analyze by LC-MS/MS because of the small, hydrophilic nature of peptides produced by tryptic digestion. Although bottom-up methods permit identification of several H1 phosphorylation events, these peptides are not useful for observing the combinatorial post-translational modification (PTM) patterns on the protein of interest. To complement the information provided by bottom-up MS, we utilized a top-down MS/MS workflow to permit identification and quantitation of H1 proteoforms related to the progression of breast cells through the cell cycle. Histones H1.2 and H1.4 were observed in MDA-MB-231 metastatic breast cells, whereas an additional histone variant, histone H1.3, was identified only in nonneoplastic MCF-10A cells. Progressive phosphorylation of histone H1.4 was identified in both cell lines at mitosis (M phase). Phosphorylation occurred first at S172 followed successively by S187, T18, T146, and T154. Notably, phosphorylation at S173 of histone H1.2 and S172, S187, T18, T146, and T154 of H1.4 significantly increases during M phase relative to S phase, suggesting that these events are cell cycle-dependent and may serve as markers for proliferation. Finally, we report the observation of the H1.2 SNP variant A18V in MCF-10A cells.

Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadrupole Mass Spectrometry

The electrodynamic ion funnel facilitates efficient focusing and transfer of charged particles in the higher-pressure regions (e.g., ion source interfaces) of mass spectrometers, thus providing increased sensitivity. An "off-axis" ion funnel design has been developed to reduce the source contamination and interferences from, e.g. ESI droplet residue and other poorly focused neutral or charged particles with very high mass-to-charge ratios. In this study, a dual ion funnel interface consisting of an orthogonal higher pressure electrodynamic ion funnel (HPIF) and an ion funnel trap combined with a triple quadrupole mass spectrometer was developed and characterized. An orthogonal ion injection inlet and a repeller plate electrode was used to direct ions to an ion funnel HPIF at a pressure of 9-10 Torr. Key factors for the HPIF performance characterized included the effects of RF amplitude, the DC gradient, and operating pressure. Compared to the triple quadrupole standard interface more than 4-fold improvement in the limit of detection for the direct quantitative MS analysis of low abundance peptides was observed. The sensitivity enhancement in liquid chromatography selected reaction monitoring (LC-SRM) analyses of low-abundance peptides spiked into a highly complex mixture was also compared with that obtained using both a commercial S-lens interface and an in-line dual-ion funnel interface.

Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations

A new Structures for Lossless Ion Manipulations (SLIM) module, having electrode arrays patterned on a pair of parallel printed circuit boards (PCB), was constructed and utilized to investigate capabilities for ion trapping at a pressure of 4 Torr. Positive ions were confined by application of RF voltages to a series of inner rung electrodes with alternating phase on adjacent electrodes, in conjunction with positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potentials applied to the inner rung electrodes to control the ion transport and accumulation inside the ion trapping region. We show that ions can be trapped and accumulated with up to 100% efficiency, stored for at least 5 h with no significant losses, and then could be rapidly ejected from the SLIM trap. The present results provide a foundation for the development of much more complex SLIM devices that facilitate extended ion manipulations.

Design and performance of a high-flux electrospray ionization source for ion soft landing

A high-flux electrospray source enables deposition of micrograms of mass-selected ions for studies in catalysis and materials science.

Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer

Enhancements to the ion source and transfer optics of our 9.4 T Fourier transform ion cyclotron resonance (ICR) mass spectrometer have resulted in improved ion transmission efficiency for more sensitive mass measurement of complex mixtures at the MS and MS/MS levels. The tube lens/skimmer has been replaced by a dual ion funnel and the following octopole by a quadrupole for reduced ion cloud radial expansion before transmission into a mass-selective quadrupole. The number of ions that reach the ICR cell is increased by an order of magnitude for the funnel/quadrupole relative to the tube lens/skimmer/octopole.

Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations

Structures for lossless ion manipulations (SLIM) have recently demonstrated the ability for near lossless ion focusing, transfer, and trapping in subatmospheric pressure regions. While lossless ion manipulations are advantageously applied to the applications of ion mobility separations and gas phase reactions, ion introduction through ring electrode ion funnels or more conventional ion optics to SLIM can involve discontinuities in electric fields or other perturbations that result in ion losses. In this work, we developed and investigated a new funnel design that aims to seamlessly couple to SLIM at the funnel exit. This rectangular ion funnel (RIF) was initially evaluated by ion simulations, fabricated utilizing printed circuit board technology, and tested experimentally. The RIF was integrated to a SLIM-time of flight (TOF) MS system, and the operating parameters, including RF, DC bias of the RIF electrodes, and electric fields for effectively interfacing with a SLIM, were characterized. The RIF provided a 2-fold sensitivity increase without significant discrimination over a wide m/z range and well matched to that of SLIM, along with greatly improved SLIM operational stability.

Improving the sensitivity of mass spectrometry by using a new sheath flow electrospray emitter array at subambient pressures

Arrays of chemically etched emitters with individualized sheath gas capillaries were developed to enhance electrospray ionization (ESI) efficiency at subambient pressures. By incorporating the new emitter array in a subambient pressure ionization with nanoelectrospray (SPIN) source, both ionization efficiency and ion transmission efficiency were significantly increased, providing enhanced sensitivity in mass spectrometric analyses. The SPIN source eliminates the major ion losses of conventional ESI-mass spectrometry (MS) interfaces by placing the emitter in the first reduced pressure region of the instrument. The new ESI emitter array design developed in this study allows individualized sheath gas around each emitter in the array making it possible to generate an array of uniform and stable electrosprays in the subambient pressure (10 to 30 Torr) environment for the first time. The utility of the new emitter arrays was demonstrated by coupling the emitter array/SPIN source with a time of flight (TOF) mass spectrometer. The instrument sensitivity was compared under different ESI source and interface configurations including a standard atmospheric pressure single ESI emitter/heated capillary, single emitter/SPIN and multi-emitter/SPIN configurations using an equimolar solution of nine peptides. The highest instrument sensitivity was observed using the multi-emitter/SPIN configuration in which the sensitivity increased with the number of emitters in the array. Over an order of magnitude MS sensitivity improvement was achieved using multi-emitter/SPIN compared with using the standard atmospheric pressure single ESI emitter/heated capillary interface.

Improving ion mobility measurement sensitivity by utilizing helium in an ion funnel trap

Ion mobility instruments that utilize nitrogen as buffer gas are often preceded by an ion trap and accumulation region that also uses nitrogen, and for different inert gases, no significant effects upon performance are expected for ion mobility spectrometry (IMS) of larger ions. However, we have observed significantly improved performance for an ion funnel trap upon adding helium; the signal intensities for higher m/z species were improved by more than an order of magnitude compared to using pure nitrogen. The effect of helium upon IMS resolving power was also studied by introducing a He/N₂ gas mixture into the drift cell, and in some cases, a slight improvement was observed compared to pure N₂. The improvement in signal can be largely attributed to faster and more efficient ion ejection into the drift tube from the ion funnel trap.

Practical Considerations and Current Limitations in Quantitative Mass Spectrometry-based Proteomics

Quantitative mass spectrometry (MS)-based proteomics continues to evolve through advances in sample preparation, chemical and biochemical reagents, instrumentation, and software. The breadth of proteomes and biological applications combined with unique experimental goals makes optimizing MS-based proteomics workflows a daunting task. Several MS-based instrument platforms are commercially available with LC-MS/MS being the most common for quantitative proteomics studies. Although the direction of LC-MS/MS instrumentation development is toward more user-friendly interfaces, there remain fundamental aspects of the technology that can be optimized for improving data quality. The intent of this chapter is to provide an introductory framework for understanding some of the more significant LC-MS/MS experimental conditions that can influence quantitative MS-based proteomics measurements, including electrospray ionization (ESI) bias and ion transmission efficiency. Because each commercial LC-MS/MS system is unique with regard to ESI source, transmission optics, ion isolation and trapping, ion fragmentation, and mass analysis, the use of design of experiments (DoE) is discussed as a potential approach for efficiently optimizing multiple inter-related factors.

Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer

Ion mobility-mass spectrometry measurements which describe the gas-phase scaling of molecular size and mass are of both fundamental and pragmatic utility. Fundamentally, such measurements expand our understanding of intrinsic intramolecular folding forces in the absence of solvent. Practically, reproducible transport properties, such as gas-phase collision cross-section (CCS), are analytically useful metrics for identification and characterization purposes. Here, we report 594 CCS values obtained in nitrogen drift gas on an electrostatic drift tube ion mobility-mass spectrometry (IM-MS) instrument. The instrument platform is a newly developed prototype incorporating a uniform-field drift tube bracketed by electrodynamic ion funnels and coupled to a high resolution quadrupole time-of-flight mass spectrometer. The CCS values reported here are of high experimental precision (±0.5% or better) and represent four chemically distinct classes of molecules (quaternary ammonium salts, lipids, peptides, and carbohydrates), which enables structural comparisons to be made between molecules of different chemical compositions for the rapid “omni-omic” characterization of complex biological samples. Comparisons made between helium and nitrogen-derived CCS measurements demonstrate that nitrogen CCS values are systematically larger than helium values; however, general separation trends between chemical classes are retained regardless of the drift gas. These results underscore that, for the highest CCS accuracy, care must be exercised when utilizing helium-derived CCS values to calibrate measurements obtained in nitrogen, as is the common practice in the field.

Design, simulation and evaluation of improved air amplifier incorporating an ion funnel for nano-ESI MS

An improved air amplifier design that takes advantage of the combined effects of aerodynamic and electrodynamic focusing was developed to couple a nanoelectrospray ionisation (nano-ESI) source and the heated mass spectrometer inlet to improve the sensitivity of a mass spectrometer. The new design comprises an electrodynamic ion funnel integrated into the main air pathway of the air amplifier to more effectively focus and transmit gas-phase ions from the nano-ESI source into the heated mass spectrometer inlet. Numerical computational fluid dynamics simulations were carried out using a commercial software package, ANSYS FLUENT, to provide more detailed information about the device's performance. The gas flow field as well as the electric field patterns and the Lagrangian ion motion were conveniently simulated using this single package and custom-written, user-defined functions. Experimental results show a nearly five-fold improvement in reserpine ion intensity with the air amplifier operated at a nitrogen gauge pressure of 40 kPa and no direct current (DC) or radiofrequency (RF) potentials applied to the ion funnel when the distance between the electrospray emitter and sampling inlet tube was 24 mm, as compared to direct sample infusion from the same distance without the air amplifier. More importantly, a nearly three-fold additional gain in ion intensity was measured when both DC and RF potentials were co-applied, resulting in more than a 13-fold overall ion intensity gain which could be attributed to the combined air amplifier aerodynamic and ion funnel electrodynamic focusing effect.

Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry

Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for analyzing complex biological samples. To fully utilize the information obtained from these three measurement dimensions, informatics tools based on the accurate mass and time tag methodology were modified to incorporate ion mobility spectrometry drift times for peptides observed in human serum. In this work a reference human serum database was created for 12,139 peptides and populated with the monoisotopic mass, liquid chromatography normalized elution time, and ion mobility spectrometry drift time(s) for each. We demonstrate that the use of three dimensions for peak matching during the peptide identification process resulted in an increased numbers of identifications and a lower false discovery rate relative to only using the mass and normalized elution time dimensions.

Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies

Quantitative plasma proteomics, through the use of targeted MRM-MS and isotopically labeled standards, is emerging as a popular technique to address biological- and biomedical-centered queries. High precision and accuracy are essential in such measurements, particularly in protein biomarker research where translation to the clinic is sought. Standardized procedures and routine performance evaluation of all stages of the workflow (both pre-analytical and analytical) are therefore imperative to satisfy these requisites and enable high inter-laboratory reproducibility and transferability. In this review, we first discuss the pre-analytical and analytical variables that can affect the precision and accuracy of ‘absolute’ quantitative plasma proteomic measurements. Proposed strategies to limit such variability will then be highlighted and unmet needs for future exploration will be noted. Although there is no way to conduct a truly comprehensive review on this broad, rapidly changing topic, we have highlighted key aspects and included references to review articles on various sub-topics.

Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS

We demonstrate the direct coupling of transient capillary isotachophoresis/capillary zone electrophoresis (CITP/CZE) with a high-sensitivity triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode for sample quantitation. The capability of CITP/CZE for in situ sample enrichment and separation has been shown to significantly improve the analytical figures of merit. A linear dynamic range spanning 4 orders of magnitude was observed. An average signal-to-noise ratio (S/N) of 49.6 was observed for 50 amol of targeted peptide in the presence of a complex and much more abundant bovine serum albumin (BSA) digest. Correlation of variation (CV) of <10% for peak area was measured from triplicate sample analyses at 50 pM peptide concentration, showing good reproducibility of this online CITP/CZE-SRM mass spectrometry (MS) platform, and with limit of quantitation (LOQ) demonstrated to be well below 50 pM.

Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure

Human serum glycan profiling with mass spectrometry (MS) has been employed to study several disease conditions and is demonstrating promise in, for example, clinical biomarker discovery. However, the low glycan ionization efficiency and the large dynamic range of glycan concentrations in human sera can hinder comprehensive profiling. In particular, large glycans are problematic because they are present at low concentrations and are prone to fragmentation. Here we show that, following liquid chromatographic separation on graphite columns, subambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile in comparison with the conventional atmospheric pressure electrospray ionization (ESI)-MS with a heated capillary inlet. Notably, the ions generated by the SPIN interface were observed at higher charge states for approximately half of the annotated glycans. Out of a total of 130 detected glycans, 34 were only detected with the SPIN-MS, resulting in improved coverage of glycan families as well as of glycans with larger numbers of labile monosaccharides.

The influence of electrospray ion source design on matrix effects

This study investigates to which extent the design of electrospray ion sources influences the susceptibility to matrix effects (MEs) in liquid chromatography-tandem mass spectrometry (LC-MS/MS). For this purpose, MEs were measured under comparable conditions (identical sample extracts, identical LC column, same chromatographic method and always positive ion mode) on four LC-MS/MS instrument platforms. The instruments were combined with five electrospray ion sources, viz. Turbo Ion Spray, Turbo V(TM) Source, Standard ESI, Jet Stream ESI and Standard Z-Spray Source. The comparison of MEs could be made at all retention times because the method of permanent postcolumn infusion was applied. The MEs ascertained for 45 pesticides showed for each electrospray ion source the same pattern, i.e. the same number of characteristic signal suppressions at equivalent retention times in the chromatogram. The Turbo Ion Spray (off-axis geometry), Turbo V(TM) Source (orthogonal geometry) and the Standard Z-Spray Source (double orthogonal geometry) did not differ much in their susceptibility to MEs. The Jet Stream ESI (orthogonal geometry) reaches a higher sensitivity by an additional heated sheath gas, but suffers at the same time from significantly stronger signal suppressions than the comparable Standard ESI (orthogonal geometry) without sheath gas. No relation between source geometry and extent of signal suppression was found in this study.

Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics

Selected reaction monitoring (SRM) - also known as multiple reaction monitoring (MRM) - has emerged as a promising high-throughput targeted protein quantification technology for candidate biomarker verification and systems biology applications. A major bottleneck for current SRM technology, however, is insufficient sensitivity for, e.g. detecting low-abundance biomarkers likely present at the low ng/mL to pg/mL range in human blood plasma or serum, or extremely low-abundance signaling proteins in cells or tissues. Herein, we review recent advances in methods and technologies, including front-end immunoaffinity depletion, fractionation, selective enrichment of target proteins/peptides including posttranslational modifications, as well as advances in MS instrumentation which have significantly enhanced the overall sensitivity of SRM assays and enabled the detection of low-abundance proteins at low- to sub-ng/mL level in human blood plasma or serum. General perspectives on the potential of achieving sufficient sensitivity for detection of pg/mL level proteins in plasma are also discussed.

Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface

In this work, the subambient pressure ionization with nanoelectrospray (SPIN) ion source and interface, which operates at ~15-30 Torr, is demonstrated to be compatible with gradient reversed-phase liquid chromatography-MS applications, exemplified here with the analysis of complex samples (a protein tryptic digest and a whole cell lysate). A low liquid chromatographic flow rate (100-400 nL/min) allowed stable electrospray to be established while avoiding electrical breakdown. Efforts to increase the operating pressure of the SPIN source relative to previously reported designs prevented solvent freezing and enhanced charged cluster/droplet desolvation. A 5- to 12-fold improvement in sensitivity relative to a conventional atmospheric pressure nanoelectrospray ionization (ESI) source was obtained for detected peptides.

Pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer

Liquid chromatography (LC)-triple quadrupole mass spectrometers operating in a multiple reaction monitoring (MRM) mode are increasingly used for quantitative analysis of low-abundance analytes in highly complex biochemical matrixes. After development and selection of optimum MRM transitions, sensitivity and data quality limitations are largely related to mass spectral peak interferences from sample or matrix constituents and statistical limitations at low number of ions reaching the detector. Herein, we report on a new approach to enhancing MRM sensitivity by converting the continuous stream of ions from the ion source into a pulsed ion beam through the use of an ion funnel trap (IFT). Evaluation of the pulsed MRM approach was performed with a tryptic digest of Shewanella oneidensis strain MR-1 spiked with several model peptides. The sensitivity improvement observed with the IFT coupled in to the triple quadrupole instrument is based on several unique features. First, ion accumulation radio frequency (rf) ion trap facilitates improved droplet desolvation, which is manifested in the reduced background ion noise at the detector. Second, signal amplitude for a given transition is enhanced because of an order-of-magnitude increase in the ion charge density compared to a continuous mode of operation. Third, signal detection at the full duty cycle is obtained, as the trap use eliminates dead times between transitions, which are inevitable with continuous ion streams. In comparison with the conventional approach, the pulsed MRM signals showed 5-fold enhanced peak amplitude and 2-3-fold reduced chemical background, resulting in an improvement in the limit of detection (LOD) by a factor of ∼4-8.