Capillary-based multi nanoelectrospray emitters: improvements in ion transmission efficiency and implementation with capillary reversed-phase LC-ESI-MS

Let’s Get Small: Miniaturizing Separations for Single-Cell Analysis

Direct profiling of biochemical expression within single cells provides insights into cellular processes that are lost when ensemble averages are measured across populations of cells. Advanced separations coupled with mass spectrometry (MS) can now quantify more than 1000 proteins within single cells. Further miniaturization of separations will greatly extend the reach of single-cell proteomics, metabolomics, and lipidomics, but key challenges in instrumentation, column technology, and ionization sources must be addressed.

Characterization of Spray Modes and Factors Affecting the Ionization Efficiency of Paper Spray Ionization

In this study, we systematically evaluated the factors affecting the ionization efficiency of paper spray ionization (PSI), such as electric field, solvent supply rate, and paper thickness and hydrophobicity. The observed paper spray plume was classified into three modes: single cone-jet, multi-jet, and rim-jet modes. With the increase in the spraying voltage, the spray plume appeared in order of single cone-jet, multi-jet, and rim-jet modes. The rim-jet mode exhibited the lowest standard deviation and high ionization efficiency among the three spray modes. The main parameter determining the spray mode was the charge density of the droplets generated by paper spray, which depends on the electric field and solvent supply rate. A thicker paper reduced the electric repulsion between the jets and lowered the threshold voltage to reach the rim-jet mode. Lowering the solvent supply rate caused mode transitions from the single cone-jet to the rim-jet, possibly due to the increased droplet charge density. The hydrophobic modification on a paper substrate led to a different ionization mechanism or electrostatic spray ionization at low applied voltages.

Quantification and evaluation of ion transmission efficiency in two-stage vacuum chamber miniature mass spectrometer

Miniature mass spectrometer is more compact and portable than traditional commercial mass spectrometry, with more potential for application outside the laboratory. However, a miniature mass spectrometer is less sensitive than a commercial instrument, limiting its application scenarios. The ion transmission efficiency of the instrument is an essential factor affecting the sensitivity. Still, there are few works of literature on the quantitative study of the ion transmission efficiency of each component from a systematic perspective. In this paper, the Faraday cup coupled with a microcurrent signal testing instrument was used to measure the ions generated by nanoelectrospray ionization (nano-ESI), which have successfully gone through several components. Then the ion transmission efficiency of each component was quantified. Results showed that the front lens had the highest ion transmission efficiency of 39.7%, whereas the inlet and skimmer had the lowest ion transfer efficiency of 0.8% and 17.1%. Next, the influence of control parameters on ion transmission efficiency of critical components was investigated. If optimized, the ion funnel and the skimmer had the potential to improve their transmission efficiency by 120% and 79%, respectively. This paper shows the decreasing intensity distribution of ions in the whole transmission process and the transmission efficiency of each component, which can guide for improving the sensitivity of the miniature mass spectrometer.

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.

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.

Electric modeling and characterization of pulsed high-voltage nanoelectrospray ionization sources by a miniature ion trap mass spectrometer

A better understanding of nanoelectrospray ionization (nano-ESI) would be beneficial in further improving the performances of nano-ESI. In this work, the pulsed high-voltage (HV) nano-ESI has been electrically modeled and then systematically characterized by both voltage-current and mass spectrometry measurements. First, the equivalent resistance of a nano-ESI source changes with respect to both emitter tip diameter and the HV applied. Increased voltage could improve both spray current and ionization efficiency of the pulsed HV nano-ESI. Compared with conventional DC HV method, a pulsed HV has less heating effect on the capillary tip and thus allowing the application of a much higher voltage onto a nano-ESI source. As a result, a pulsed HV nano-ESI could further boost the ionization efficiency of nano-ESI by employing even higher voltages than conventional DC nano-ESI sources.

Toward Confirmatory On-Site Real-Time Detection of Emerging Drugs Using Portable Ultrafast Capillary Electrophoresis Mass Spectrometry

Currently, law enforcement agencies rely upon presumptive tests such as color tests (or spot tests) for on-site, real-time identification of forensic evidence, such as controlled substances. These tests are simple and easy to use and require no instrumentation. However, they are unreliable and have a large false positive rate. On the other hand, confirmatory tests are done in analytical laboratories using sophisticated instrumentation by expert analysts, and have lower false positive rates. However, they are bulky and impractical for on-site real-time analysis. To provide more accurate identification of forensic evidence on-site, in real-time, it is important to develop portable confirmatory instrumentation using information-rich technologies. Moreover, because the analysis of controlled substances could be complicated by the existence of various isomers (including optical isomers) it is desirable that the portable instruments have the capability to separate structural and optical isomers of the controlled substances, because scheduling is some times dependent upon which isomer is present. To this end, we have developed a portable ultrafast capillary electrophoresis (UFCE) system for the separation of controlled substances and their structural and optical isomers. The UFCE instrument has an integrated porous tip for facile interfacing with electrospray ionization mass spectrometry. The technique has been successfully applied to the analysis of mixtures of several controlled substances such as amphetamines, cathinones, nor-mephedrone, and pregabalin and their optical isomers in about a minute.

Fourier transform ion mobility spectrometry with multinozzle emitter array electrospray ionization

Fourier transform ion mobility spectrometry (FT-IMS) is a useful multiplexing method for improving the duty cycle (DC) of IMS from 1 to 25% when using an entrance and exit ion gate to modulate the ion current with a synchronized square wave chirp.

Non-tapered PTFE capillary as robust and stable nanoelectrospray emitter for electrospray ionization mass spectrometry

RATIONALE

The successful implementation of electrospray ionization mass spectrometry (ESI-MS) largely relies on the physical and chemical properties of electrospray emitters. Current ESI emitters based on pulled glass or fused-silica capillaries suffer from complicated fabrication procedures and short lifetime because of clogging and breakage problems. ESI emitters with high robustness, easy operation, and low cost are in great demand.

METHODS

We proposed to directly use non-pulled and non-tapered polytetrafluoroethylene (PTFE) capillaries as nanoelectrospray emitters. We evaluated and studied the performance of PTFE emitters under different flow rates and ESI voltages. Their applications in direct infusion and liquid chromatography (LC)-MS analysis were achieved.

RESULTS

High stable electrospray (relative standard deviation of total ion current intensity <5%) can be obtained at flow rates from 100 nL/min to 1500 nL/min and at ESI voltages from 1.8 kV to 2.9 kV using non-tapered PTFE emitters. Different types of samples including small-molecule drugs, peptides, and proteins can be detected with high sensitivity. LC-MS analysis of two model peptides was successfully demonstrated.

CONCLUSIONS

We have demonstrated that a non-tapered PTFE capillary can be a promising ESI emitter for both direct infusion and LC-MS analysis. We envision it could find broad applications in high-throughput MS analysis fields, such as drug screening and proteomics, where robust and reproducible operations are essentially required. Copyright © 2016 John Wiley & Sons, Ltd.

Numerical analysis of ion-funnel transmission efficiency in an API-MS system with a continuum/microscopic approach

A multi-step numerical approach is used to analyze the efficiency of an ion-funnel to transport ions over a wide range of m/z. A continuum approach based on the solution of the Navier-Stokes equations is applied to model the gas flow through a capillary connecting the atmospheric and subatmospheric sections of a mass spectrometer. A microscopic, fully kinetic approach based on the solution of the Boltzmann equation is used to examine the ion and gas transport through an ion-funnel kept at a 0.1-3 Torr pressure to the quadrupole section kept at a 0.01 Torr pressure. In addition to aerodynamic drag, the developed approach takes into account the combined effect of the DC field driving the ions downstream toward the funnel exit, the rf field confining the ions in radial direction, and the space charge causing ion repulsion. The sensitivity of the ion transmission to the gas pressure in the ion-funnel, the rf, and the total ion current injected to the funnel from capillary nozzle is shown. Graphical Abstract ᅟ.

A pulsed pinhole atmospheric pressure interface for simplified mass spectrometry instrumentation with enhanced sensitivity

RATIONALE

A proof-of-concept pulsed pinhole atmospheric pressure interface, namely PP-API, was developed and characterized for mass spectrometry instrumentation.

METHODS

The PP-API was analyzed and optimized theoretically with respect to gas flow rate, opening force and dimensions. A PP-API interfaced mass spectrometry system was then constructed and tested.

RESULTS

As a discontinuous pressure interface, the PP-API allows efficient ion transfer from atmosphere pressure ionization sources to ion traps directly. Both nano-ESI and APCI ionization sources have been successfully integrated with the PP-API interface for the detection of volatile, organic, peptide and polymer samples. The use of multiple ionization sources has also been demonstrated to enhance signal intensity, as well as avoid charge competitions in ionization sources.

CONCLUSIONS

With simplified geometry and high ion transfer efficiency, this PP-API would enable miniaturized mass spectrometry systems with high sensitivity.

Compatibility of highly sulfated cyclodextrin with electrospray ionization at low nanoliter/minute flow rates and its application to capillary electrophoresis/electrospray ionization mass spectrometric analysis of cathinone derivatives and their optical isomers

RATIONALE

Sodium salts of cyclodextrins are commonly used in capillary electrophoresis/mass spectrometry (CE/MS) analysis of illicit drugs and their optical isomers. To avoid the suppression effect of cyclodextrins under electrospray ionization (ESI), the partial filling technique (PFT) is commonly utilized, which has a limited resolution. Low-flow nano-ESI has been shown to reduce the suppression effect of the salts. To test the compatibility of low-flow ESI with a background electrolyte (BGE) containing sodium salts of cyclodextrin, sheathless narrow capillary CE/MS with flow rates of low nanoliters/minute (nL/min) was applied to the separation and detection of cathinones and their positional and optical isomers for the first time.

METHODS

Low-flow sheathless CE/MS using a 20-µm-i.d. capillary in conjunction with a porous tip interface was used for the separation of cathinone derivatives and their optical isomers. Highly sulfated γ-cyclodextrin (HS-γ-CD) in conjunction with (+)-18-crown-6-tetracarboxylic acid ((+)-18-C-6-TCA) was used as the BGE and an ion trap mass spectrometer operating in full scan mode was utilized.

RESULTS

Utilizing low flow rate (~10 nL/min) sheathless CE/MS, the use of the sodium salt of HS-γ-CD as the BGE was compared with the same solution using PFT. The relative and absolute sensitivity of detection of cathinones were about the same, indicating that under low-flow sheathless CE/MS there was no significant suppression due to the existence of HS-γ-CD in the electrospray process. However, enhanced resolution of cathinone derivatives and their positional and optical isomers was observed when the solution of HS-γ-CD was used as the BGE. The enhanced resolution was because of the presence of the HS-γ-CD in the entire capillary during the analysis. The addition of 15 mM (+)-18-C-6-TCA to the BGE containing HS-γ-CD further enhanced the resolution resulting in separation of all cathinones and their positional and optical isomers.

CONCLUSIONS

A novel CE/MS technique has been introduced that combines low-flow sheathless CE/MS, with HS-γ-CD and 15 mM (+)-18-C-6-TCA as the BGE for separation of cathinone derivatives as well as their positional and optical isomers.

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.

Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria

In a time in which the spread of multidrug resistant microorganisms is ever increasing, there is a need for fast and unequivocal identification of suspect organisms to supplement existing techniques in the clinical laboratory, especially in single bacterial colonies. Mass-spectrometry coupled with efficient peptide separation techniques offer great potential for identification of resistant-related proteins in complex microbiological samples in an unbiased manner. Here, we developed a capillary electrophoresis-electrospray ionization-tandem mass spectrometry CE-ESI-MS/MS bottom-up proteomics workflow for sensitive and specific peptide analysis with the emphasis on the identification of β-lactamases (carbapenemases OXA-48 and KPC in particular) in bacterial species. For this purpose, tryptic peptides from whole cell lysates were analyzed by sheathless CE-ESI-MS/MS and proteins were identified after searching of the spectral data against bacterial protein databases. The CE-ESI-MS/MS workflow was first evaluated using a recombinant TEM-1 β-lactamase, resulting in 68% of the amino acid sequence being covered by 20 different unique peptides. Subsequently, a resistant and susceptible Escherichia coli lab strain were analyzed and based on the observed β-lactamase peptides, the two strains could easily be discriminated. Finally, the method was tested in an unbiased setup using a collection of in-house characterized OXA-48 (n = 17) and KPC (n = 10) clinical isolates. The developed CE-ESI-MS/MS method was able to identify the presence of OXA-48 and KPC in all of the carbapenemase positive samples, independent of species and degree of susceptibility. Four negative controls were tested and classified as negative by this method. Furthermore, a number of extended-spectrum beta-lactamases (ESBL) were identified in the same analyses, confirming the multiresistant character in 19 out of 27 clinical isolates. Importantly, the method performed equally well on protein lysates from single colonies. As such, it demonstrates CE-ESI-MS/MS as a potential next generation mass spectrometry platform within the clinical microbiology laboratory.

Proteomic analysis of saliva in HIV-positive heroin addicts reveals proteins correlated with cognition

The prevalence of HIV-associated neurocognitive disorders (HAND) remains high despite effective antiretroviral therapies. Multiple etiologies have been proposed over the last several years to account for this phenomenon, including the neurotoxic effects of antiretrovirals and co-morbid substance abuse; however, no underlying molecular mechanism has been identified. Emerging evidence in several fields has linked the gut to brain diseases, but the effect of the gut on the brain during HIV infection has not been explored. Saliva is the most accessible gut biofluid, and is therefore of great scientific interest for diagnostic and prognostic purposes. This study presents a longitudinal, liquid chromatography-mass spectrometry-based quantitative proteomics study investigating saliva samples taken from 8 HIV-positive (HIV⁺), 11 −negative (HIV⁻) heroin addicts. In addition, saliva samples were investigated from 11 HIV⁻, non-heroin addicted healthy controls. In the HIV⁺ group, 58 proteins were identified that show significant correlations with cognitive scores, implicating disruption of protein quality control pathways by HIV. Notably, only one protein from the HIV⁻ heroin addict cohort showed a significant correlation with cognitive scores, and no proteins correlated with cognitive scores in the healthy control group. In addition, the majority of correlated proteins have been shown to be associated with exosomes, allowing us to propose that the salivary glands and/or oral epithelium may modulate brain function during HIV infection through the release of discrete packets of proteins in the form of exosomes.

Picoelectrospray ionization mass spectrometry using narrow-bore chemically etched emitters

Electrospray ionization mass spectrometry (ESI-MS) at flow rates below ~10 nL/min has been only sporadically explored because of difficulty in reproducibly fabricating emitters that can operate at lower flow rates. Here we demonstrate narrow orifice chemically etched emitters for stable electrospray at flow rates as low as 400 pL/min. Depending on the analyte concentration, we observe two types of MS signal response as a function of flow rate. At low concentrations, an optimum flow rate is observed slightly above 1 nL/min, whereas the signal decreases monotonically with decreasing flow rates at higher concentrations. For example, consumption of 500 zmol of sample yielded signal-to-noise ratios ~10 for some peptides. In spite of lower MS signal, the ion utilization efficiency increases exponentially with decreasing flow rate in all cases. Significant variations in ionization efficiency were observed within this flow rate range for an equimolar mixture of peptide, indicating that ionization efficiency is an analyte-dependent characteristic for the present experimental conditions. Mass-limited samples benefit strongly from the use of low flow rates and avoiding unnecessary sample dilution. These findings have important implications for the analysis of trace biological samples.

Comparing and combining capillary electrophoresis electrospray ionization mass spectrometry and nano-liquid chromatography electrospray ionization mass spectrometry for the characterization of post-translationally modified histones

We present the first comprehensive capillary electrophoresis electrospray ionization mass spectrometry (CESI-MS) analysis of post-translational modifications derived from H1 and core histones. Using a capillary electrophoresis system equipped with a sheathless high-sensitivity porous sprayer and nano-liquid chromatography electrospray ionization mass spectrometry (nano-LC-ESI-MS) as two complementary techniques, we characterized H1 histones isolated from rat testis. Without any pre-separation of the perchloric acid extraction, a total of 70 different modified peptides, including 50 phosphopeptides, were identified in the rat linker histones H1.0, H1a-H1e, and H1t. Out of the 70 modified H1 histone peptides, 27 peptides could be identified with CESI-MS only, and 11 solely with LC-ESI-MS. Immobilized metal-affinity chromatography enrichment prior to MS analysis yielded a total of 55 phosphopeptides; 22 of these peptides could be identified only by CESI-MS, and 19 only by LC-ESI-MS, showing the complementarity of the two techniques. We mapped 42 H1 modification sites, including 31 phosphorylation sites, of which 8 were novel sites. For the analysis of core histones, we chose a different strategy. In a first step, the sulfuric-acid-extracted core histones were pre-separated using reverse-phase high-performance liquid chromatography. Individual rat testis core histone fractions obtained in this way were digested and analyzed via bottom-up CESI-MS. This approach yielded the identification of 42 different modification sites including acetylation (lysine and N(α)-terminal); mono-, di-, and trimethylation; and phosphorylation. When we applied CESI-MS for the analysis of intact core histone subtypes from butyrate-treated mouse tumor cells, we were able to rapidly detect their degree of modification, and we found this method very useful for the separation of isobaric trimethyl and acetyl modifications. Taken together, our results highlight the need for additional techniques for the comprehensive analysis of post-translational modifications. CESI-MS is a promising new proteomics tool as demonstrated by this, the first comprehensive analysis of histone modifications, using rat testis as an example.

Multinozzle emitter array chips for small-volume proteomics

High-throughput multiplexed proteomics of small-volume biospecimens will generate new opportunities in theranostics. Achieving parallel top-down and bottom-up mass spectrometry analyses of target proteins using a unified apparatus will improve proteome characterization. We have developed a novel silicon-based microfluidic device, multinozzle emitter array chip (MEA chip), as a new platform for small-volume proteomics using liquid chromatography-nanoelectrospray ionization mass spectrometry (LC-nanoESI-MS). We demonstrate parallel, on-chip, and online LC-MS analysis of hemoglobin and its tryptic digests directly from microliters of blood, achieving a detection limit of less than 5 red blood cells. Our MEA chip will enable clinical proteomics of small-volume samples.

Microfluidic chip-based liquid chromatography coupled to mass spectrometry for determination of small molecules in bioanalytical applications

The development and integration of microfabricated liquid chromatography (LC) microchips have increased dramatically in the last decade due to the needs of enhanced sensitivity and rapid analysis as well as the rising concern on reducing environmental impacts of chemicals used in various types of chemical and biochemical analyses. Recent development of microfluidic chip-based LC mass spectrometry (chip-based LC-MS) has played an important role in proteomic research for high throughput analysis. To date, the use of chip-based LC-MS for determination of small molecules, such as biomarkers, active pharmaceutical ingredients (APIs), and drugs of abuse and their metabolites, in clinical and pharmaceutical applications has not been thoroughly investigated. This mini-review summarizes the utilization of commercial chip-based LC-MS systems for determination of small molecules in bioanalytical applications, including drug metabolites and disease/tumor-associated biomarkers in clinical samples as well as adsorption, distribution, metabolism, and excretion studies of APIs in drug discovery and development. The different types of commercial chip-based interfaces for LC-MS analysis are discussed first and followed by applications of chip-based LC-MS on biological samples as well as the comparison with other LC-MS techniques.

Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels

Morphine has long been known to have immunosuppressive properties in vivo, but the molecular and immunologic changes induced by it are incompletely understood. To explore how these changes interact with lentiviral infections in vivo, animals from two nonhuman primate species (African green monkeys and pigtailed macaques) were provided morphine and studied using a systems biology approach. Biological specimens were obtained from multiple sources (e.g. lymph node, colon, cerebrospinal fluid, and peripheral blood) before and after the administration of morphine (titrated up to a maximum dose of 5 mg/kg over a period of 20 days). Cellular immune, plasma cytokine, and proteome changes were measured and morphine-induced changes in these parameters were assessed on an interorgan, interindividual, and interspecies basis. In both species, morphine was associated with decreased levels of Ki-67(+) T-cell activation but with only minimal changes in overall T-cell counts, neutrophil counts, and NK cell counts. Although changes in T-cell maturation were observed, these varied across the various tissue/fluid compartments studied. Proteomic analysis revealed a morphine-induced suppressive effect in lymph nodes, with decreased abundance of protein mediators involved in the functional categories of energy metabolism, signaling, and maintenance of cell structure. These findings have direct relevance for understanding the impact of heroin addiction and the opioids used to treat addiction as well as on the potential interplay between opioid abuse and the immunological response to an infective agent.

Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values.

Cyanobacteria have been promoted as platforms for biofuel production due to their useful physiological properties such as photosynthesis, relatively rapid growth rates, ability to accumulate high amounts of intracellular compounds and tolerance to extreme environments. However, development of a computational model is an important step to synthesize biochemical, physiological and regulatory understanding of photoautotrophic metabolism (either qualitatively or quantitatively) at a systems level, to make metabolic engineering of these organisms tractable. When integrated with other genome-scale data (e.g., expression data), numerical simulations can provide experimentally testable predictions of carbon fluxes and reductant partitioning to different biosynthetic pathways and macromolecular synthesis. This work is the first to computationally explore the interactions between components of photosynthetic and respiratory systems in detail. In silico predictions obtained from model analysis provided insights into the effects of light quantity and quality upon fluxes through electron transport pathways, alternative pathways for reductant consumption and carbon metabolism. The model will not only serve as a platform to develop genome-scale metabolic models for other cyanobacteria, but also as an engineering tool for manipulation of photosynthetic microorganisms to improve biofuel production.

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.

Multiple electrosprays generated from a single polycarbonate microstructured fibre

Electrospray ionization (ESI) has been invaluable to the mass spectrometric detection of biomolecules, due largely to the sensitivity afforded by the ionization technique. Lower flow rates, e.g. in the nanoelectrospray regime, result in smaller initial electrosprayed droplets, leading to higher ionization efficiency and greater signal. One approach to improving sensitivity without lowering flow rate is to generate multiple electrosprays (MESs) from the same sample, essentially splitting one larger flow into smaller flows in the nanoESI regime. Presented here is a series of novel MES emitters in the form of polycarbonate fibres. Based on microstructured fibre (MSF) technology whereby a set of homogeneous parallel channels are formed in a heat-drawn fibre intended to conduct light, a custom design was fabricated in which 3, 6, 9 and 12 holes were arranged in a radial pattern to prevent inhomogeneities in the electric field. The MSFs have dimensions that are compatible with current standards in nanoESI equipment, and the tip is more compatible with standard MS orifices than other larger multielectrospray emitters. By measuring the spray current provided by the various emitters under the same solvent/voltage/total flow rate conditions, a plot was obtained clearly demonstrating the expected dependence on the square root of the number of holes, i.e. the number of independent electrosprays. With this firm proof of principle using this design/format, further effort is justified in developing similar emitters in alternative materials that better prevent surface wetting and allow greater hole density, ultimately leading to greater signal enhancement.

Mass spectrometry of peptides and proteins from human blood

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

Multinozzle emitter arrays for nanoelectrospray mass spectrometry

Mass spectrometry (MS) is the enabling technology for proteomics and metabolomics. However, dramatic improvements in both sensitivity and throughput are still required to achieve routine MS-based single cell proteomics and metabolomics. Here, we report the silicon-based monolithic multinozzle emitter array (MEA) and demonstrate its proof-of-principle applications in high-sensitivity and high-throughput nanoelectrospray mass spectrometry. Our MEA consists of 96 identical 10-nozzle emitters in a circular array on a 3 in. silicon chip. The geometry and configuration of the emitters, the dimension and number of the nozzles, and the micropillar arrays embedded in the main channel can be systematically and precisely controlled during the microfabrication process. Combining electrostatic simulation and experimental testing, we demonstrated that sharpened-end geometry at the stem of the individual multinozzle emitter significantly enhanced the electric fields at its protruding nozzle tips, enabling sequential nanoelectrospray for the high-density emitter array. We showed that electrospray current of the multinozzle emitter at a given total flow rate was approximately proportional to the square root of the number of its spraying-nozzles, suggesting the capability of high MS sensitivity for multinozzle emitters. Using a conventional Z-spray mass spectrometer, we demonstrated reproducible MS detection of peptides and proteins for serial MEA emitters, achieving sensitivity and stability comparable to the commercial capillary emitters. Our robust silicon-based MEA chip opens up the possibility of a fully integrated microfluidic system for ultrahigh-sensitivity and ultrahigh-throughput proteomics and metabolomics.

High-throughput analysis using gated multi-inlet mass spectrometry

Gated multi-inlet mass spectrometry is introduced for high-throughput chemical analysis. In this design, multiple high-pressure liquid chromatography (HPLC) columns or capillary electrophoresis (CE) capillaries are attached to multiple electrosprayers (one for each column or capillary) that spray toward a gated multi-inlet time-of-flight mass spectrometer (TOF-MS). Although all of the sprayers are spraying continuously, only one inlet is exposed at any given time for a specific duration set by the MS data system. The gated multi-sprayer, multi-inlet design significantly enhances the performance of the multi-ESI, multi-inlet TOF-MS with minimal cost and reduces analysis time. The gated multi-sprayer, multi-inlet design was applied to the investigation of column-to-column reproducibility of multiple HPLCs using a peptide mixture and to the simultaneous analysis of four protein digests. In addition, it was applied to the analysis of peptide mixtures using eight CE capillaries. The gated multi-inlet MS has several advantages compared to our previous non-gated multi-inlet MS. For example, because only one inlet is open at one time, the original manufacturer's inlet inner diameter and pumping system can be used, which enhances the sensitivity of detection for each inlet and minimizes the manufacturing cost. In addition, the number of inlets can be increased as desired. The maximum number of liquid streams that can be concurrently analyzed is limited by: (1) the number of inlets, (2) the chromatographic (electrophoretic) peak width, and (3) how fast the gate can move from one position to the next.

Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections

The host proteome response and molecular mechanisms that drive disease in vivo during infection by a human isolate of the highly pathogenic avian influenza virus (HPAI) and 1918 pandemic influenza virus remain poorly understood. This study presents a comprehensive characterization of the proteome response in cynomolgus macaque (Macaca fascicularis) lung tissue over 7 days of infection with HPAI (the most virulent), a reassortant virus containing 1918 hemagglutinin and neuraminidase surface proteins (intermediate virulence), or a human seasonal strain (least virulent). A high-sensitivity two-dimensional liquid chromatography-tandem mass spectroscopy strategy and functional network analysis were implemented to gain insight into response pathways activated in macaques during influenza virus infection. A macaque protein database was assembled and used in the identification of 35,239 unique peptide sequences corresponding to approximately 4,259 proteins. Quantitative analysis identified an increase in expression of 400 proteins during viral infection. The abundance levels of a subset of these 400 proteins produced strong correlations with disease progression observed in the macaques, distinguishing a "core" response to viral infection from a "high" response specific to severe disease. Proteome expression profiles revealed distinct temporal response kinetics between viral strains, with HPAI inducing the most rapid response. While proteins involved in the immune response, metabolism, and transport were increased rapidly in the lung by HPAI, the other viruses produced a delayed response, characterized by an increase in proteins involved in oxidative phosphorylation, RNA processing, and translation. Proteomic results were integrated with previous genomic and pathological analysis to characterize the dynamic nature of the influenza virus infection process.

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.

Enhanced sensitivity for selected reaction monitoring mass spectrometry-based targeted proteomics using a dual stage electrodynamic ion funnel interface

Selected reaction monitoring mass spectrometry (SRM-MS) is playing an increasing role in quantitative proteomics and biomarker discovery studies as a method for high throughput candidate quantification and verification. Although SRM-MS offers advantages in sensitivity and quantification compared with other MS-based techniques, current SRM technologies are still challenged by detection and quantification of low abundance proteins (e.g. present at ∼10 ng/ml or lower levels in blood plasma). Here we report enhanced detection sensitivity and reproducibility for SRM-based targeted proteomics by coupling a nanospray ionization multicapillary inlet/dual electrodynamic ion funnel interface to a commercial triple quadrupole mass spectrometer. Because of the increased efficiency in ion transmission, significant enhancements in overall signal intensities and improved limits of detection were observed with the new interface compared with the original interface for SRM measurements of tryptic peptides from proteins spiked into non-depleted mouse plasma over a range of concentrations. Overall, average SRM peak intensities were increased by ∼70-fold. The average level of detection for peptides also improved by ∼10-fold with notably improved reproducibility of peptide measurements as indicated by the reduced coefficients of variance. The ability to detect proteins ranging from 40 to 80 ng/ml within mouse plasma was demonstrated for all spiked proteins without the application of front-end immunoaffinity depletion and fractionation. This significant improvement in detection sensitivity for low abundance proteins in complex matrices is expected to enhance a broad range of SRM-MS applications including targeted protein and metabolite validation.

The ion funnel: theory, implementations, and applications

The electrodynamic ion funnel has enabled the manipulation and focusing of ions in a pressure regime (0.1-30 Torr) that has challenged traditional approaches, and provided the basis for much greater mass spectrometer ion transmission efficiencies. The initial ion funnel implementations aimed to efficiently capture ions in the expanding gas jet of an electrospray ionization interface and radially focus them for efficient transfer through a conductance limiting orifice. We review the improvements in fundamental understanding of ion motion in ion funnels, the evolution in its implementations that have brought the ion funnel to its current state of refinement, as well as applications of the ion funnel for purposes such as ion trapping, ion cooling, low pressure electrospray, and ion mobility spectrometry.

Integration of Proteomic-Based Tools for Improved Biomarkers of Myocardial Injury

Background: Given the mounting evidence in favor of early pharmacologic and catheter-based interventions for patients across the spectrum of acute coronary syndromes, discovering novel diagnostically sensitive and specific biomarkers that provide biochemical proof of early or reversible myocardial injury could have a substantial positive impact on patient care.

Content: To address unmet needs in disease biomarkers, investigators have turned to proteomics approaches. We describe advances in proteomics discovery technologies based on liquid chromatography–tandem mass spectrometry that facilitate the unbiased analysis of low-abundance blood proteins. We detail the development of emerging techniques to enhance the biomarker verification process, such as accurate inclusion mass screening, stable isotope dilution–multiple reaction monitoring–mass spectrometry (SID-MRM-MS), and stable isotope standards with capture by antipeptide antibodies, which combines the advantages of specific immunoaffinity enrichment of a target peptide with the structural specificity and quantitative capabilities of SID-MRM-MS. We highlight new assays incorporating these techniques for troponin I, a representative low-abundance cardiac biomarker, and interleukin-33, an emerging novel marker of myocardial stress for which no existing ELISA exists. We demonstrate that troponin I and interleukin-33 peptides have a linear, dynamic range spanning 4 orders of magnitude and limits of detection of approximately 0.5 μg/L back-calculated to the protein concentration.

Conclusions: There remain important unmet diagnostic and prognostic needs in cardiology. Advances in technology may allow proteomics to play a vital role in the discovery and validation of novel biomarkers to help fill those needs.

Nanoelectrospray emitters: trends and perspective

The benefits of electrospray ionization are many, including sensitivity, robustness, simplicity and the ability to couple continuous flow methods with mass spectrometry. The technique has seen further improvement by lowering flow rates to the nanoelectrospray regime (<1,000 nL/min), where sample consumption is minimized and sensitivity increases. The move to nanoelectrospray has required a shift in the design of the electrospray source which has mostly involved the emitter itself. The emitter has seen an evolution in architecture as the shape and geometry of the device have proved pivotal in the formation of sufficiently small droplets for sensitive MS detection at these flow rates. There is a clear movement toward the development of emitters that produce multiple Taylor cones. Such multielectrospray emitters have been shown to provide enhanced sensitivity and sample utilization. This article reviews the development of nanoelectrospray emitters, including factors such as geometry and the manner of applying voltage. Designs for emitters that take advantage of multielectrospray are emphasized.

Improving FAIMS sensitivity using a planar geometry with slit interfaces

Differential mobility spectrometry or field asymmetric waveform ion mobility spectrometry (FAIMS) is gaining broad acceptance for analyses of gas-phase ions, especially in conjunction with largely orthogonal separation methods such as mass spectrometry (MS) and/or conventional (drift tube) ion mobility spectrometry. In FAIMS, ions are filtered while passing through a gap between two electrodes that may have planar or curved (in particular, cylindrical) geometry. Despite substantial inherent advantages of the planar configuration and its near-universal adoption in current stand-alone FAIMS devices, commercial FAIMS/MS systems have employed curved FAIMS geometries that can be more effectively interfaced to MS. Here we report a new planar (p-) FAIMS design with slit-shaped entrance and exit apertures that substantially increase ion transmission in and out of the analyzer. The entrance slit interface effectively couples p-FAIMS to multi-emitter electrospray ionization (ESI) sources, improving greatly the ion current introduced to the device and allowing liquid flow rates up to approximately 50 microL/min. The exit slit interface increases the transmission of ribbon-shaped ion beams output by the p-FAIMS to downstream stages such as a MS. Overall, the ion signal in ESI/FAIMS/MS analyses increases by over an order of magnitude without affecting FAIMS resolution.

Metabolomics-based methods for early disease diagnostics

The emerging field of metabolomics, in which a large number of small-molecule metabolites from body fluids or tissues are detected quantitatively in a single step, promises immense potential for early diagnosis, therapy monitoring and for understanding the pathogenesis of many diseases. Metabolomics methods are mostly focused on the information-rich analytical techniques of NMR spectroscopy and mass spectrometry (MS). Analysis of the data from these high-resolution methods using advanced chemometric approaches provides a powerful platform for translational and clinical research and diagnostic applications. In this review, the current trends and recent advances in NMR- and MS-based metabolomics are described with a focus on the development of advanced NMR and MS methods, improved multivariate statistical data analysis and recent applications in the area of cancer, diabetes, inborn errors of metabolism and cardiovascular diseases.