Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry

Tuning the Internal Energy of Ions Produced by Atmospheric and High-Pressure Electrospray by Modulating the Gas Throughput into the First Vacuum Stage

In a high-pressure environment, electrospray ionization (ESI) can be achieved without discharge between the emitter and the counter electrode, thus enabling the generation of gas-phase ions from liquid with high surface tension, such as pure water, which requires a high onset voltage for stable ESI. In this study, the ion dissociation during the transferring of ions/charged droplets from a superatmospheric pressure environment to vacuum has been systematically investigated using benzyl ammonium thermometer ions. The ion source pressure did not affect the internal energy distribution of ions, whereas the gas throughput into the first vacuum stage clearly influences the internal energy distribution of the ions. The increase in the gas throughput increased the density of molecules/atoms presented in ion transfer/focusing electrodes located in the first vacuum stage. As a result, the mean free path of ions in the first vacuum stage decreases, and the energy of ions decreases by decreasing the kinetic energy involved in each collision between ions and residue gas. The gas throughput into the first vacuum stage is found to describe the internal energy distribution of ions associated with the local conditions more quantitatively instead of using the measured pressure of the vacuum stage, which is different from the effective local pressure. This study also demonstrated the controlled dissociation of ions using the ion transfer settings of the instrument in combination with ion inlet tubes of different sizes.

A 3D-printed sub-atmospheric pressure electrospray ionization source for robust, facile, and flexible mass spectrometry analysis

The operation and performance of electrospray ionization (ESI) is affected by the surrounding environment. In this study, a compact sub-atmospheric pressure ESI (SAP-ESI) source was designed and fabricated using the 3D printing method. This source has a simple structure and is easy to operate, as the sample solution and auxiliary gas are continuously sucked into the source through the pressure difference. The compact and enclosed ionization chamber can reduce the fluctuation of the surrounding gas flow to ensure a remarkably stable (< 3%) electrospray. Moreover, the source can offer variable SAP conditions for ESI analysis. The yield of analyte ions increases with decreasing pressure, while the production of background ions is suppressed under these conditions. In the analysis of protein samples, SAP-ESI can increase the yield and charge state of ions, which may be due to the reduction of proton transfer between charged proteins and surrounding gas. The SAP-ESI source was then used to continuously monitor the extract aqueous solution of tea leaves, and to detect the carbendazim residues on the apple surface by coupling with the liquid extraction surface analysis technique. Experimental results demonstrate that the developed SAP-ESI is a stable, practical, and versatile ionization technique.

A tutorial: Laserspray ionization and related laser-based ionization methods for use in mass spectrometry

This Tutorial is to provide a summary of parameters useful for successful outcomes of laserspray ionization (LSI) and related methods that employ a laser to ablate a matrix:analyte sample to produce highly charged ions. In these methods the purpose of the laser is to transfer matrix-analyte clusters into the gas phase. Ions are hypothesized to be produced by a thermal process where emitted matrix:analyte gas-phase particles/clusters are charged and loss of matrix from the charged particles leads to release of the analyte ions into the gas phase. The thermal energy responsible for the charge-separation process is relatively low and not necessarily supplied by the laser; a heated inlet tube linking atmospheric pressure with the first vacuum stage of a mass spectrometer is sufficient. The inlet becomes the "ion source", and inter alia, pressure, temperature, and the matrix, which can be a solid, liquid, or combinations, become critical parameters. Injecting matrix:analyte into a heated inlet tube using laser ablation, a shockwave, or simply tapping, all produce the similar mass spectra. Applications are provided that showcase new opportunities in the field of mass spectrometry.

Mass spectrometry-based targeted proteomics for analysis of protein mutations

Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.

Unbiased spatial proteomics with single-cell resolution in tissues

Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify the entire complement of proteins in cells or tissues. Here, we review challenges and recent advances in the LC-MS-based analysis of minute protein amounts, down to the level of single cells. Application of this technology revealed that single-cell transcriptomes are dominated by stochastic noise due to the very low number of transcripts per cell, whereas the single-cell proteome appears to be complete. The spatial organization of cells in tissues can be studied by emerging technologies, including multiplexed imaging and spatial transcriptomics, which can now be combined with ultra-sensitive proteomics. Combined with high-content imaging, artificial intelligence and single-cell laser microdissection, MS-based proteomics provides an unbiased molecular readout close to the functional level. Potential applications range from basic biological questions to precision medicine.

Navigate Flying Molecular Elephants Safely to the Ground: Mass-Selective Soft Landing up to the Mega-Dalton Range by Electrospray Controlled Ion-Beam Deposition

The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to T_total = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.

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.

Electrospray Ionization Inside the Ion Inlet Tube: Multijet Mode Operation

We investigated the electrospray ionization inside the narrow channel of the ion inlet tube. An insulating emitter capillary made of fused silica with a 0.2 mm outer diameter was inserted into the ion inlet tubes with a 0.5 and 0.6 mm inner diameter to aspirate all the charged droplets. A custom-made ion inlet tube with two side holes near its entrance is used to observe the spraying condition. The spray current is measured and monitored during the MS acquisition using isolation amplifiers. Because the emitter is cylindrically surrounded in close proximity by the metallic inner wall, it is difficult to obtain a stable and symmetric Taylor cone with its apex at the center of the emitter. Instead, a stable operation under a flow rate of 1-4 μL/min is found to be in the form of a multicone-jet mode with two or more Taylor cones anchoring around the rim of the emitter. The emitted charged droplet jets are dragged from hitting the wall by the fast-flowing air inside the inlet tube. Comparison with the typical cone-jet and multijet mode operated several millimeters outside the inlet capillary shows signal enhancements for protein standards.

An overview of biological applications and fundamentals of new inlet and vacuum ionization technologies

RATIONALE

The developments of new ionization technologies based on processes previously unknown to mass spectrometry (MS) have gained significant momentum. Herein we address the importance of understanding these unique ionization processes, demonstrate the new capabilities currently unmet by other methods, and outline their considerable analytical potential.

METHODS

The inlet and vacuum ionization methods of solvent-assisted ionization (SAI), matrix-assisted ionization (MAI), and laserspray ionization can be used with commercial and dedicated ion sources producing ions from atmospheric or vacuum conditions for analyses of a variety of materials including drugs, lipids, and proteins introduced from well plates, pipet tips and plate surfaces with and without a laser using solid or solvent matrices. Mass spectrometers from various vendors are employed.

RESULTS

Results are presented highlighting strengths relative to ionization methods of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization. We demonstrate the utility of multi-ionization platforms encompassing MAI, SAI, and ESI and enabling detection of what otherwise is missed, especially when directly analyzing mixtures. Unmatched robustness is achieved with dedicated vacuum MAI sources with mechanical introduction of the sample to the sub-atmospheric pressure (vacuum MAI). Simplicity and use of a wide array of matrices are attained using a conduit (inlet ionization), preferably heated, with sample introduction from atmospheric pressure. Tissue, whole blood, urine (including mouse, chicken, and human origin), bacteria strains and chemical on-probe reactions are analyzed directly and, especially in the case of vacuum ionization, without concern of carryover or instrument contamination.

CONCLUSIONS

Examples are provided highlighting the exceptional analytical capabilities associated with the novel ionization processes in MS that reduce operational complexity while increasing speed and robustness, achieving mass spectra with low background for improved sensitivity, suggesting the potential of this simple ionization technology to drive MS into areas currently underserved, such as clinical and medical applications.

Current perspectives on supercharging reagents in electrospray ionization mass spectrometry

In electrospray ionization mass spectrometry (ESI-MS), analytes are introduced into the mass spectrometer in typically aqueous-organic solvent mixtures, including pH modifiers. One mechanism for improving the signal intensity and simultaneously increasing the generation of higher charge-state ions is the inclusion of small amounts (approx. <0.5% v/v mobile phase solution) of charge-inducing or supercharging reagents, such as m-nitrobenzyl alcohol, o-nitrobenzyl alcohol, m-nitrobenzonitrile, m-(trifluoromethyl)-benzyl alcohol and sulfolane. We explore the direct and indirect (colligative properties) that have been proposed as responsible for their modes of action during ESI. Of the many theorized mechanisms of ESI, we re-visit the three most popular and highlight how they are impacted by supercharging observations on small ions to large molecules including proteins. We then provide a comprehensive list of 34 supercharging reagents that have been demonstrated in ESI experiments. We include an additional 19 potential candidate isomers as supercharging reagents and comment on their broad physico-chemical properties. It is becoming increasingly obvious that advances in technology and improved ion source design, analyzers e.g. the use of ion mobility, ion trap, circular dichroism (CD) spectroscopy, together with computer modeling are increasing the knowledge base and, together with the untested isomers and yet-to-be unearthed ones, offer opportunities for further research and application in other areas of polymer research.

A simple illustration of the positive electrospray ionization (ESI) environment.

Single-cell Proteomics: Progress and Prospects

MS-based proteome profiling has become increasingly comprehensive and quantitative, yet a persistent shortcoming has been the relatively large samples required to achieve an in-depth measurement. Such bulk samples, typically comprising thousands of cells or more, provide a population average and obscure important cellular heterogeneity. Single-cell proteomics capabilities have the potential to transform biomedical research and enable understanding of biological systems with a new level of granularity. Recent advances in sample processing, separations and MS instrumentation now make it possible to quantify >1000 proteins from individual mammalian cells, a level of coverage that required an input of thousands of cells just a few years ago. This review discusses important factors and parameters that should be optimized across the workflow for single-cell and other low-input measurements. It also highlights recent developments that have advanced the field and opportunities for further development.

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.

Exploiting the native inspiratory ability of a mass spectrometer to improve analysis efficiency

In this study, a new approach to perform self-aspirating sampling in mass spectrometry (MS) analysis was developed by using the native inspiratory ability of a mass spectrometer. Specifically, the inspiratory channel and sampling inlet of the MS instrument were integrated into a single pathway through a sealed ionization chamber to facilitate analyte delivery and improve sample utilization. Based on this approach, combined with structural simplification and optimization, a versatile electrospray ionization (ESI) source has been constructed and characterized using different mass spectrometers. In addition to the self-aspirating ability, this source configuration can provide sub-ambient pressure (SAP) conditions for ionization, which were conducive to suppressing the background ions generated from some air-involved reactions. Moreover, it can also be used directly for electrospray-driven extraction ionization. With the SAP-ESI source, a conventional mass spectrometer enables rapid analysis of both volatiles and solutions via secondary electrospray ionization and coaxial electrospray ionization, respectively. As the compact gas pathway of the source will promote the efficient transfer and ionization of the sampled substances, the total consumption of the analyte for each analysis can be reduced to subnanogram level and a subppbv limit detection is achieved. Other demonstrated features such as the versatility, easy operation as well as simple assembly will likely contribute to the prevalence of the proposed sampling and ionization strategy.

In this study, a new approach to perform self-aspirating sampling in mass spectrometry (MS) analysis was developed by using the native inspiratory ability of a mass spectrometer.

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.

Nanoproteomics comes of age

INTRODUCTION

Nanoproteomics, which is defined as quantitative proteome profiling of small populations of cells (<5000 cells), can reveal critical information related to rare cell populations, hard-to-obtain clinical specimens, and the cellular heterogeneity of pathological tissues. Areas covered: We present a brief review of the recent technological advances in nanoproteomics. These advances include new technologies or approaches covering major areas of proteomics workflow ranging from sample isolation, sample processing, high-resolution separations, to MS instrumentation. Expert commentary: We comment on the current state of nanoproteomics and discuss perspectives on both future technological directions and potential enabling applications.

DRILL: An Electrospray Ionization-Mass Spectrometry Interface for Improved Sensitivity via Inertial Droplet Sorting and Electrohydrodynamic Focusing in a Swirling Flow

We describe the DRILL (dry ion localization and locomotion) device, which is an interface for electrospray ionization (ESI)-mass spectrometry (MS) that exploits a swirling flow to enable the use of inertial separation to prescribe different fates for electrosprayed droplets based on their size. This source adds a new approach to charged droplet trajectory manipulation which, when combined with hydrodynamic drag forces and electric field forces, provides a rich range of possible DRILL operational modes. Here, we experimentally demonstrate sensitivity improvement obtained via vortex-induced inertial sorting of electrosprayed droplets/ions: one possible mode of DRILL operation. In this mode, DRILL removes larger droplets while accelerating the remainder of the ESI plume, producing a high velocity stream of gas-enriched spray with small, highly charged droplets and ions and directing it toward the MS inlet. The improved signal-to-noise ratio (10-fold enhancement) in the detection of angiotensin I is demonstrated using the DRILL interface coupled to ESI-MS along with an improved limit of detection (10-fold enhancement, 100 picomole) in the detection of angiotensin II. The utility of DRILL has also been demonstrated by liquid chromatography (LC)-MS: a stable isotope labeled peptide cocktail was spiked into a complex native tissue extract and quantified by unscheduled multiple reaction monitoring on a TSQ Vantage. DRILL demonstrated improved signal strength (up to a 700-fold) for 8 out of 9 peptides and had no effects on the peak shape of the transitions.

Electrospray Modifications for Advancing Mass Spectrometric Analysis

Generation of analyte ions in gas phase is a primary requirement for mass spectrometric analysis. One of the ionization techniques that can be used to generate gas phase ions is electrospray ionization (ESI). ESI is a soft ionization method that can be used to analyze analytes ranging from small organics to large biomolecules. Numerous ionization techniques derived from ESI have been reported in the past two decades. These ion sources are aimed to achieve simplicity and ease of operation. Many of these ionization methods allow the flexibility for elimination or minimization of sample preparation steps prior to mass spectrometric analysis. Such ion sources have opened up new possibilities for taking scientific challenges, which might be limited by the conventional ESI technique. Thus, the number of ESI variants continues to increase. This review provides an overview of ionization techniques based on the use of electrospray reported in recent years. Also, a brief discussion on the instrumentation, underlying processes, and selected applications is also presented.

Quantifying Kinase-Specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-Gel Kinase Assay

Despite recent advancements in large-scale phosphoproteomics, methods to quantify kinase-specific phosphorylation stoichiometry of protein substrates are lacking. We developed a method to quantify kinase-specific phosphorylation stoichiometry by combining the reverse in-gel kinase assay (RIKA) with high-resolution liquid chromatography-mass spectrometry (LC-MS). Beginning with predetermined ratios of phosphorylated to nonphosphorylated protein kinase CK2 (CK2) substrate molecules, we employed ¹⁸O-labeled adenosine triphosphate (¹⁸O-ATP) as the phosphate donor in a RIKA, then quantified the ratio of ¹⁸O- versus ¹⁶O-labeled tryptic phosphopeptide using high mass accuracy mass spectrometry (MS). We demonstrate that the phosphorylation stoichiometry determined by this method across a broad percent phosphorylation range correlated extremely well with the predicted value (correlation coefficient = 0.99). This approach provides a quantitative alternative to antibody-based methods of determining the extent of phosphorylation of a substrate pool.

Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics

Liquid chromatography coupled online to nano-electrospray ionization (nESI) tandem mass spectrometry is the analytical workhorse in the field of proteome research. Dimethyl sulfoxide (DMSO) was recently shown to improve nESI efficiency by a factor of three to ten thus improving the sensitivity and coverage of proteomic experiments. However, relatively few investigations into which solvent additives promote nESI response have been performed at a proteomic scale. Here, we systematically evaluated the concept by screening about 30 compounds with various physico-chemical properties. Detailed further analysis showed that ethylene glycol performed similarly to DMSO and the results indicate that enhancing the nESI response of peptides by simple solvent additives is a valid and promising approach. Ethylene glycol may serve as a viable alternative to DMSO in applications where DMSO has disadvantages. In keeping with nESI theory, the key properties of an effective solvent additive for proteomic applications are a boiling point higher than water, low surface tension, and preferably high polarity for reversed phase LC-MS/MS applications. Graphical Abstract Ethylene glycol substantially improves peptide ionization.

Advances in targeted proteomics and applications to biomedical research

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.

Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules

Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.

Zero volt paper spray ionization mass spectrometry for direct analysis of samples on filter paper substrate

RATIONALE

Zero volt paper spray ionization (zvPSI) is a newly developed sample introduction/ionization technique for mass spectrometry (MS), which combines favorable features of paper spray ionization (PSI) and solvent-assisted inlet ionization (SAII). With a simple platform similar to PSI, zvPSI allows direct MS analysis of a broad type of samples (liquid, (semi-)solid, and imprint) without applying voltage.

METHODS

In zvPSI-MS, a rectangular paper slip was used as a sample loader, extraction medium, and droplet emitter to introduce sample extract into the inlet of a mass spectrometer. For (semi-)solid and imprint samples, analyte(s) was directly extracted with solvent and instantaneously introduced into a mass spectrometer by aspiration. Solution samples were analyzed after being dried-up or by dispensing directly onto paper. Ionization was achieved by SAII and ionized molecules were detected by an ion-trap mass spectrometer.

RESULTS

The developed method allowed direct voltage-free MS analysis of samples on filter paper substrate. Favorable features of PSI and SAII were successfully combined, such as fast data acquisition, flexible sample handlings, and direct extraction capability from solid samples (PSI), with no need for external high-voltage, laser, or nebulizing gas to convert analytes into gas-phase ions (SAII). Comparable to PSI and SAII, a wide variety of compounds such as amino acids, peptides, lipids and synthetic polymers were shown to be analyzed.

CONCLUSIONS

The developed method (zvPSI-MS) expanded the analytical utility of PSI and SAII to voltage-free direct MS analysis of a broad type of samples (liquid, (semi-)solid, and imprint).

A fundamental study on the [(μ-Cl)3Mg2(THF)6]+ dimer electrolytes for rechargeable Mg batteries

The long sought solvated [MgCl](+) species in the Mg-dimer electrolytes was characterized by soft mass spectrometry. The presented study provides an insightful understanding on the electrolyte chemistry of rechargeable Mg batteries.

Coupling an electrospray source and a solids probe/chemical ionization source to a selected ion flow tube apparatus

A new ion source region has been constructed and attached to a variable temperature selected ion flow tube. The source features the capabilities of electron impact, chemical ionization, a solids probe, and electrospray ionization. The performance of the instrument is demonstrated through a series of reactions from ions created in each of the new source regions. The chemical ionization source is able to create H3O(+), but not as efficiently as similar sources with larger apertures. The ability of this source to support a solids probe, however, greatly expands our capabilities. A variety of rhenium cations and dications are created from the solids probe in sufficient abundance to study in the flow tube. The reaction of Re(+) with O2 proceeds with a rate constant that agrees with the literature measurements, while the reaction of Re2(2+) is found to charge transfer with O2 at about 60% of the collision rate; we have also performed calculations that support the charge transfer pathway. The electrospray source is used to create Ba(+), which is reacted with N2O to create BaO(+), and we find a rate constant that agrees with the literature.

Microfabricated ultrarapid desalting device for nanoelectrospray ionization mass spectrometry

Salt removal is a prerequisite for electrospray ionization mass spectrometry (ESI-MS) analysis of biological samples. Rapid desalting and a low volume connection to an electrospray tip are required for time-resolved measurements. We have developed a microfabricated desalting device that meets both requirements, thus providing the foundational technology piece for transient ESI-MS measurements of complex biological liquid specimens. In the microfabricated device, the sample flows in a channel separated from a higher flow rate, salt-free counter solution by a monolithically integrated nanoporous alumina membrane, which can support pressure differences between the flow channels of over 600 kPa. Salt is removed by exploiting the large difference in diffusivities between salts and the typical ESI-MS target bioanalytes, e.g., peptides and proteins. We demonstrate the capability to remove 95% of salt from a sample solution in ∼1 s while retaining sufficiently high concentration of a relatively low molecular weight protein, cytochrome-c, for ESI-MS detection.

On the ionization and ion transmission efficiencies of different ESI-MS interfaces

The achievable sensitivity of electrospray ionization mass spectrometry (ESI-MS) is largely determined by the ionization efficiency in the ESI source and ion transmission efficiency through the ESI-MS interface. These performance characteristics are difficult to evaluate and compare across multiple platforms as it is difficult to correlate electrical current measurements to actual analyte ions reaching the detector of a mass spectrometer. We present an effective method to evaluate the overall ion utilization efficiency of an ESI-MS interface by measuring the total gas-phase ion current transmitted through the interface and correlating it to the observed ion abundance measured in the corresponding mass spectrum. Using this method, we systematically studied the ion transmission and ionization efficiencies of different ESI-MS interface configurations, including a single emitter/single inlet capillary, single emitter/multi-inlet capillary, and a subambient pressure ionization with nanoelectrospray (SPIN) MS interface with a single emitter and an emitter array, respectively. Our experimental results indicate that the overall ion utilization efficiency of SPIN-MS interface configurations exceeds that of the inlet capillary-based ESI-MS interface configurations.

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.

A novel planar ion funnel design for miniature ion optics

The novel planar ion funnel (PIF) design presented in this article emphasizes simple fabrication, assembly, and operation, making it amenable to extreme miniaturization. Simulations performed in SIMION 8.0 indicate that ion focusing can be achieved by using a gradient of electrostatic potentials on concentric metal rings in a plane. A prototype was fabricated on a 35 × 35 mm custom-designed printed circuit board (PCB) with a center hole for ions to pass through and a series of concentric circular metal rings of increasing diameter on the front side of the PCB. Metal vias on the PCB electrically connected each metal ring to a resistive potential divider that was soldered on the back of the PCB. The PIF was tested at 5.5 × 10(-6) Torr in a vacuum test setup that was equipped with a broad-beam ion source on the front and a micro channel plate (MCP) ion detector on the back of the PIF. The ion current recorded on the MCP anode during testing indicated a 23× increase in the ion transmission through the PIF when electric potentials were applied to the rings. These preliminary results demonstrate the functionality of a 2D ion funnel design with a much smaller footprint and simpler driving electronics than conventional 3D ion funnels. Future directions to improve the design and a possible micromachining approach to fabrication are discussed in the conclusions.

High sensitivity combined with extended structural coverage of labile compounds via nanoelectrospray ionization at subambient pressures

Subambient pressure ionization with nanoelectrospray (SPIN) has proven to be effective in producing ions with high efficiency and transmitting them to low pressures for increased sensitivity in mass spectrometry (MS) analysis. Here we present evidence that the SPIN source not only improves MS sensitivity but also facilitates the detection of more labile compounds. The gentleness of conventional heated capillary electrospray ionization (ESI) and the SPIN designs was compared in conjunction with the liquid chromatography mass spectrometry (LC–MS) analysis of colominic acid and N-glycans containing sialic acid. Prior experiments conducted with the SPIN interface demonstrated the ability to detect labile glycans such as heavily sialylated and polysialic acid N-glycans, which are difficult to detect with a conventional ESI-MS interface. Colominic acid is a mixture of sialic acid polymers of different lengths containing labile glycosidic linkages between monomer units necessitating a gentle ion source. These labile covalent bonds may display similar behavior to sialic acid chains in N-glycans during MS analysis. By coupling the SPIN source with high-resolution mass spectrometry and using advanced data processing tools, we demonstrate much extended coverage of sialic acid polymer chains as compared to conventional ESI-MS and the ability to detect sialic acid containing N-glycans without the need of sample derivatization. In addition, we show that SPIN-LC–MS is effective in elucidating polymer features with high efficiency and high sensitivity previously unattainable by the conventional ESI-LC–MS methods.

High pressure nanoelectrospray ionization mass spectrometry for analysis of aqueous solutions

Nanoelectrospray ionization (nanoESI) with a very fine emitter and nanoliter solution flow rate is known to be suitable for aqueous solutions. However, under atmospheric pressure, its stability with aqueous solutions is not always guaranteed particularly in the negative ion mode where corona and arc discharge tend to occur more easily. Electrical discharge can be quenched to a certain extent by adding electron scavenging gases like SF6 or CO2 to the ion source. The onset potential that is required to induce the discharge also increases with an increase of gas pressure. Recently, we have reported on a series of high pressure electrospray ion sources that were stable in both positive and negative ion modes using air or N2 as the working gas. In this paper, we compare the performance of nanoelectrospray under atmospheric pressure and super-atmospheric pressure for the analysis of samples in aqueous solution. The comparative study was performed using the same ion source chamber that could be pressurized up to 6 bar. The pressure in the first pumping stage of the mass spectrometer was kept constant when the ion source pressure was changed by using an additional pump with variable pumping speed. High pressure nanoESI optimized at 2-3 bar demonstrated a 3-5 times improvement in ion signal intensity compared to atmospheric pressure nanoESI, and the signal stability was significantly improved particularly in the negative mode.

Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry

The N-glycan diversity of human serum glycoproteins, i.e., the human blood serum N-glycome, is both complex and constrained by the range of glycan structures potentially synthesizable by human glycosylation enzymes. The known glycome, however, has been further limited by methods of sample preparation, available analytical platforms, e.g., based upon electrospray ionization-mass spectrometry (ESI-MS), and software tools for data analysis. In this report several improvements have been implemented in sample preparation and analysis to extend ESI-MS glycan characterization and to include polysialylated N-glycans. Sample preparation improvements included acidified, microwave-accelerated, PNGase F N-glycan release to promote lactonization, and sodium borohydride reduction, that were both optimized to improve quantitative yields and conserve the number of glycoforms detected. Two-stage desalting (during solid phase extraction and on the analytical column) increased sensitivity by reducing analyte signal division between multiple reducing-end-forms or cation adducts. Online separations were improved by using extended length graphitized carbon columns and adding TFA as an acid modifier to a formic acid/reversed phase gradient, providing additional resolving power and significantly improved desorption of both large and heavily sialylated glycans. To improve MS sensitivity and provide gentler ionization conditions at the source-MS interface, subambient pressure ionization with nanoelectrospray (SPIN) was utilized. When these improved methods are combined together with the Glycomics Quintavariate Informed Quantification (GlyQ-IQ) recently described (Kronewitter et al. Anal. Chem. 2014, 86, 6268-6276), we are able to significantly extend glycan detection sensitivity and provide expanded glycan coverage. We demonstrated the application of these advances in the context of the human serum glycome, and for which our initial observations included the detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans.

In situ SIMS and IR spectroscopy of well-defined surfaces prepared by soft landing of mass-selected ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3](2+) (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.

Differential mobility spectrometry with nanospray ion source as a compact detector for small organics and inorganics

Electrospray ionization (ESI) is an important tool in chemical and biochemical survey and targeted analysis in many applications. For chemical detection and identification electrospray is usually used with mass spectrometry (MS). However, for screening and monitoring of chemicals of interest in light, low power field-deployable instrumentation, an alternative detection technology with chemical selectivity would be highly useful, especially since small, lightweight, chip-based gas and liquid chromatographic technologies are being developed. Our initial list of applications requiring portable instruments includes chemical surveys on Mars, medical diagnostics based on metabolites in biological samples, and water quality analysis. In this report, we evaluate ESI-Differential Mobility Spectrometry (DMS) as a compact, low-power alternative to MS detection. Use of DMS for chemically-selective detection of ESI suffers in comparison with mass spectrometry because portable MS peak capacity is greater than that of DMS by 10X or more, but the development of light, fast chip chromatography offers compensating resolution. Standalone DMS provides the chemical selectivity familiar from DMS-MS publications, and exploits the sensitivity of ion detection. We find that sub-microliter-per-minute flows and a correctly-designed interface prepare a desolvated ion stream that enables DMS to act as an effective ion filter. Results for a several small organic biomarkers and metabolites, including citric acid, azelaic acid, n-hexanoylglycine, thymidine, and caffeine, as well as compounds such as dinitrotoluene and others, have been characterized and demonstrate selective detection. Water-quality-related halogen-containing anions, fluoride through bromate, contained in liquid samples are also isolated by DMS. A reaction-chamber interface is highlighted as most practical for portable ESI-DMS instrumentation.

Matrix assisted ionization in vacuum, a sensitive and widely applicable ionization method for mass spectrometry

An astonishingly simple new method to produce gas-phase ions of small molecules as well as proteins from the solid state under cold vacuum conditions is described. This matrix assisted ionization vacuum (MAIV) mass spectrometry (MS) method produces multiply charged ions similar to those that typify electrospray ionization (ESI) and uses sample preparation methods that are nearly identical to matrix-assisted laser desorption/ionization (MALDI). Unlike these established methods, MAIV does not require a laser or voltage for ionization, and unlike the recently introduced matrix assisted ionization inlet method, does not require added heat. MAIV-MS requires only introduction of a crystalline mixture of the analyte incorporated with a suitable small molecule matrix compound such as 3-nitrobenzonitrile directly to the vacuum of the mass spectrometer. Vacuum intermediate pressure MALDI sources and modified ESI sources successfully produce ions for analysis by MS with this method. As in ESI-MS, ion formation is continuous and, without a laser, little chemical background is observed. MAIV, operating from a surface offers the possibility of significantly improved sensitivity relative to atmospheric pressure ionization because ions are produced in the vacuum region of the mass spectrometer eliminating losses associated with ion transfer from atmospheric pressure to vacuum. Mechanistic aspects and potential applications for this new ionization method are discussed.

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.

A mechanism for ionization of nonvolatile compounds in mass spectrometry: considerations from MALDI and inlet ionization

Mechanistic arguments relative to matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) address observations that predominately singly charged ions are detected. However, recently a matrix assisted laser ablation method, laserspray ionization (LSI), was introduced that can use the same sample preparation and laser as MALDI, but produce highly charged ions from proteins. In MALDI, ions are generated from neutral molecules by the photon energy provided to a matrix, while in LSI ions are produced inside a heated inlet tube linking atmospheric pressure and the first vacuum region of the mass spectrometer. Some LSI matrices also produce highly charged ions with MALDI ion sources operated at intermediate pressure or high vacuum. The operational similarity of LSI to MALDI, and the large difference in charge states observed by these methods, provides information of fundamental importance to proposed ionization mechanisms for LSI and MALDI. Here, we present data suggesting that the prompt and delayed ionization reported for vacuum MALDI are both fast processes relative to producing highly charged ions by LSI. The energy supplied to produce these charged clusters/droplets as well as their size and time available for desolvation are determining factors in the charge states of the ions observed. Further, charged droplets/clusters may be a common link for ionization of nonvolatile compounds by a variety of MS ionization methods, including MALDI and LSI.

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.

A new approach to high sensitivity liquid chromatography-mass spectrometry of peptides using nanoflow solvent assisted inlet ionization

Liquid chromatography (LC) solvent assisted inlet ionization (SAII) mass spectrometry (MS) was previously reported to give good chromatographic resolution and MS detection injecting 66 ng of a BSA tryptic digest. In analogy to nano-electrospray ionization (nESI), we extend SAII LC/MS to nano-SAII (nSAII) operating at nL min(-1) flow rates and demonstrate good quality ion chromatograms and mass spectra from injection of as little as 0.7 ng of BSA digest onto a capillary LC column. Data dependent fragmentation is demonstrated for injection of 7 ng of a BSA digest. This method has advantages over nESI in ease of use and low cost as it requires no voltage and is operational without the necessity of connectors or fragile nESI emitters, although similar constricted tips can be helpful in nSAII to stabilize the signal at low nanoliter flow. At a flow rate of 0.8 μL min(-1), the only requirement for nSAII is that the exit-end of the capillary LC column be adjusted near the aperture of the heated inlet of the mass spectrometer.

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.

Solvent assisted inlet ionization: an ultrasensitive new liquid introduction ionization method for mass spectrometry

A new inlet ionization method requiring no voltage or laser, and using water, methanol, or water/organic solvent mixtures, is shown to produce mass spectra similar to those obtained with electrospray ionization (ESI) for small molecules, peptides, and proteins, at least as large as carbonic anhydrase, with sensitivity that surpasses ESI. With the use of wide mass range acquisitions at 100,000 mass resolution on an Orbitrap Exactive, detection limits below parts per trillion are obtained for small molecules such as arginine, ciprofloxacin, and acetaminophen. Low attomoles of bovine insulin consumed produced a multiply charged mass spectrum. Ions are generated, even using pure water as solvent, within the heated inlet tube linking atmospheric pressure with the first vacuum stage of the Orbitrap Exactive. The extremely high sensitivity observed at this early stage of solvent assisted inlet ionization (SAII) development suggests that inlet ionization may surpass nanoelectrospray in sensitivity but without the need for extremely low solvent flows.

Achieving 50% ionization efficiency in subambient pressure ionization with nanoelectrospray

Inefficient ionization and poor transmission of the charged species produced by an electrospray from the ambient pressure mass spectrometer source into the high vacuum region required for mass analysis significantly limits achievable sensitivity. Here, we present evidence that, when operated at flow rates of 50 nL/min, a new electrospray-based ion source operated at ∼20 Torr can deliver ∼50% of the analyte ions initially in the solution as charged desolvated species into the rough vacuum region of mass spectrometers. The ion source can be tuned to optimize the analyte signal for readily ionized species while reducing the background contribution.

Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes

In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonly used GeLC-MS/MS (1-D protein + 1-D peptide separation) method using four repetitive injections (2-D/repetitive) with a 3-D method that included solution isoelectric focusing and involved an equal number of LC-MS/MS runs. The 3-D method detected substantially more unique peptides and proteins, including higher numbers of unique peptides from low-abundance proteins, demonstrating that additional fractionation at the protein level is more effective than repetitive analyses at overcoming LC-MS/MS undersampling. Importantly, more than 90% of the 2-D/repetitive protein identifications were found in the 3-D method data in a direct protein level comparison, and the reproducibility between data sets increased to greater than 96% when factors such as database redundancy and use of rigid scoring thresholds were considered. Hence, high reproducibility of complex proteomes, such as human cancer cell lysates, readily can be achieved when using multidimensional separation methods with good depth of analysis.