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- Volume 7, 2014
Annual Review of Analytical Chemistry - Volume 7, 2014
Volume 7, 2014
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Biologically Inspired Nanofibers for Use in Translational Bioanalytical Systems
Vol. 7 (2014), pp. 23–42More LessElectrospun nanofiber mats are characterized by large surface-area-to-volume ratios, high porosities, and a diverse range of chemical functionalities. Although electrospun nanofibers have been used successfully to increase the immobilization efficiency of biorecognition elements and improve the sensitivity of biosensors, the full potential of nanofiber-based biosensing has not yet been realized. Therefore, this review presents novel electrospun nanofiber chemistries developed in fields such as tissue engineering and drug delivery that have direct application within the field of biosensing. Specifically, this review focuses on fibers that directly encapsulate biological additives that serve as immobilization matrices for biological species and that are used to create biomimetic scaffolds. Biosensors that incorporate these nanofibers are presented, along with potential future biosensing applications such as the development of cell culture and in vivo sensors.
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Analytical Approaches for Size and Mass Analysis of Large Protein Assemblies
Vol. 7 (2014), pp. 43–64More LessAnalysis of the size and mass of nanoparticles, whether they are natural biomacromolecular or synthetic supramolecular assemblies, is an important step in the characterization of such molecular species. In recent years, electrospray ionization (ESI) has emerged as a technology through which particles with masses up to 100 MDa can be ionized and transferred into the gas phase, preparing them for accurate mass analysis. Here we review currently used methodologies, with a clear focus on native mass spectrometry (MS). Additional complementary methodologies are also covered, including ion-mobility analysis, nanomechanical mass sensors, and charge-detection MS. The literature discussed clearly demonstrates the great potential of ESI-based methodologies for the size and mass analysis of nanoparticles, including very large naturally occurring protein assemblies. The analytical approaches discussed are powerful tools in not only structural biology, but also nanotechnology.
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Nano/Micro and Spectroscopic Approaches to Food Pathogen Detection
Vol. 7 (2014), pp. 65–88More LessDespite continuing research efforts, timely and simple pathogen detection with a high degree of sensitivity and specificity remains an elusive goal. Given the recent explosion of sensor technologies, significant strides have been made in addressing the various nuances of this important global challenge that affects not only the food industry but also human health. In this review, we provide a summary of the various ongoing efforts in pathogen detection and sample preparation in areas related to Fourier transform infrared and Raman spectroscopy, light scattering, phage display, micro/nanodevices, and nanoparticle biosensors. We also discuss the advantages and potential limitations of the detection methods and suggest next steps for further consideration.
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Optical Imaging of Individual Plasmonic Nanoparticles in Biological Samples
Vol. 7 (2014), pp. 89–111More LessImaging of plasmonic nanoparticles (PNP) with optical microscopy has aroused considerable attention in recent years. The unique localized surface plasmon resonance (LSPR) from metal nanoparticles facilitates the transduction of a chemical or physical stimulus into optical signals in a highly efficient way. It is therefore possible to perform chemical or biological assays at the single object level with the help of standard optical microscopes. Because the source of background noise from different samples is different, distinct imaging modalities have been developed to discern the signals of interest in complex surroundings. With these convenient yet powerful techniques, great improvements in chemical and biological assays have been demonstrated, and many interesting phenomena and dynamic processes have also been elucidated. Further development and application of optical imaging methods for plasmonic probes should lead to many exciting results in chemistry and biology in the future.
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Mass Spectrometric Analysis of Histone Proteoforms
Vol. 7 (2014), pp. 113–128More LessHistones play important roles in chromatin, in the forms of various posttranslational modifications (PTMs) and sequence variants, which are called histone proteoforms. Investigating modifications and variants is an ongoing challenge. Previous methods are based on antibodies, and because they usually detect only one modification at a time, they are not suitable for studying the various combinations of modifications on histones. Fortunately, mass spectrometry (MS) has emerged as a high-throughput technology for histone analysis and does not require prior knowledge about any modifications. From the data generated by mass spectrometers, both identification and quantification of modifications, as well as variants, can be obtained easily. On the basis of this information, the functions of histones in various cellular contexts can be revealed. Therefore, MS continues to play an important role in the study of histone proteoforms. In this review, we discuss the analysis strategies of MS, their applications on histones, and some key remaining challenges.
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Ultrafast 2D NMR: An Emerging Tool in Analytical Spectroscopy
Vol. 7 (2014), pp. 129–161More LessTwo-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry—from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.
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Electroanalysis at the Nanoscale
Vol. 7 (2014), pp. 163–181More LessThis article reviews the state of the art of silicon chip–based nanoelectrochemical devices for sensing applications. We first describe analyte mass transport to nanoscale electrodes and emphasize understanding the importance of mass transport for the design of nanoelectrode arrays. We then describe bottom-up and top-down approaches to nanoelectrode fabrication and integration at silicon substrates. Finally, we explore recent examples of on-chip nanoelectrodes employed as sensors and diagnostics, finishing with a brief look at future applications.
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Light-Emitting Diodes for Analytical Chemistry
Vol. 7 (2014), pp. 183–207More LessLight-emitting diodes (LEDs) are playing increasingly important roles in analytical chemistry, from the final analysis stage to photoreactors for analyte conversion to actual fabrication of and incorporation in microdevices for analytical use. The extremely fast turn-on/off rates of LEDs have made possible simple approaches to fluorescence lifetime measurement. Although they are increasingly being used as detectors, their wavelength selectivity as detectors has rarely been exploited. From their first proposed use for absorbance measurement in 1970, LEDs have been used in analytical chemistry in too many ways to make a comprehensive review possible. Hence, we critically review here the more recent literature on their use in optical detection and measurement systems. Cloudy as our crystal ball may be, we express our views on the future applications of LEDs in analytical chemistry: The horizon will certainly become wider as LEDs in the deep UV with sufficient intensity become available.
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Energetics-Based Methods for Protein Folding and Stability Measurements
Vol. 7 (2014), pp. 209–228More LessOver the past 15 years, a series of energetics-based techniques have been developed for the thermodynamic analysis of protein folding and stability. These techniques include Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX), pulse proteolysis, Stability of Proteins from Rates of Oxidation (SPROX), slow histidine H/D exchange, lysine amidination, and quantitative cysteine reactivity (QCR). The above techniques, which are the subject of this review, all utilize chemical or enzymatic modification reactions to probe the chemical denaturant– or temperature-induced equilibrium unfolding properties of proteins and protein-ligand complexes. They employ various mass spectrometry-, sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE)-, and optical spectroscopy–based readouts that are particularly advantageous for high-throughput and in some cases multiplexed analyses. This has created the opportunity to use protein folding and stability measurements in new applications such as in high-throughput screening projects to identify novel protein ligands and in mode-of-action studies to identify protein targets of a particular ligand.
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Ambient Femtosecond Laser Vaporization and Nanosecond Laser Desorption Electrospray Ionization Mass Spectrometry
Vol. 7 (2014), pp. 229–256More LessRecent investigations of ambient laser-based transfer of molecules into the gas phase for subsequent mass spectral analysis have undergone a renaissance resulting from the separation of vaporization and ionization events. Here, we seek to provide a snapshot of recent femtosecond (fs) duration laser vaporization and nanosecond (ns) duration laser desorption electrospray ionization mass spectrometry experiments. The former employs pulse durations of <100 fs to enable matrix-free laser vaporization with little or no fragmentation. When coupled to electrospray ionization, femtosecond laser vaporization provides a universal, rapid mass spectral analysis method requiring no sample workup. Remarkably, laser pulses with intensities exceeding 1013 W cm−2 desorb intact macromolecules, such as proteins, and even preserve the condensed phase of folded or unfolded protein structures according to the mass spectral charge state distribution, as demonstrated for cytochrome c and lysozyme. Because of the ability to vaporize and ionize multiple components from complex mixtures for subsequent analysis, near perfect classification of explosive formulations, plant tissue phenotypes, and even the identity of the manufacturer of smokeless powders can be determined by multivariate statistics. We also review the more mature field of nanosecond laser desorption for ambient mass spectrometry, covering the wide range of systems analyzed, the need for resonant absorption, and the spatial imaging of complex systems like tissue samples.
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Engineered Proteins for Bioelectrochemistry
Vol. 7 (2014), pp. 257–274More LessIt is only in the past two decades that excellent protein engineering tools have begun to meet parallel advances in materials chemistry, nanofabrication, and electronics. This is revealing scenarios from which synthetic enzymes can emerge, which were previously impossible, as well as interfaces with novel electrode materials. That means the control of the protein structure, electron transport pathway, and electrode surface can usher us into a new era of bioelectrochemistry. This article reviews the principle of electron transfer (ET) and considers how its application at the electrode, within the protein, and at a redox group is directing key advances in the understanding of protein structure to create systems that exhibit better efficiency and unique bioelectrochemistry.
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Microfluidics-Based Single-Cell Functional Proteomics for Fundamental and Applied Biomedical Applications
Vol. 7 (2014), pp. 275–295More LessWe review an emerging microfluidics-based toolkit for single-cell functional proteomics. Functional proteins include, but are not limited to, the secreted signaling proteins that can reflect the biological behaviors of immune cells or the intracellular phosphoproteins associated with growth factor–stimulated signaling networks. Advantages of the microfluidics platforms are multiple. First, 20 or more functional proteins may be assayed simultaneously from statistical numbers of single cells. Second, cell behaviors (e.g., motility) may be correlated with protein assays. Third, extensions to quantized cell populations can permit measurements of cell–cell interactions. Fourth, rare cells can be functionally identified and then separated for further analysis or culturing. Finally, certain assay types can provide a conduit between biology and the physicochemical laws. We discuss the history and challenges of the field then review design concepts and uses of the microchip platforms that have been reported, with an eye toward biomedical applications. We then look to the future of the field.
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Point-of-Care Platforms
Vol. 7 (2014), pp. 297–315More LessPoint-of-care applications are gaining increasing interest in clinical diagnostics and emergency applications. Biosensors are used to monitor the biomolecular interaction process between a disease biomarker and a recognition element such as a reagent. Essential are the quality and selectivity of the recognition elements and assay types used to improve sensitivity and to avoid nonspecific interactions. In addition, quality measures are influenced by the detection principle and the evaluation strategies. For these reasons, this review provides a survey and validation of recognition elements, assays, and various types of detection methods for point-of-care testing (POCT) platforms. Common applications of clinical parameters are discussed and considered. In this ever-changing field, a snapshot of current applications is needed. We provide such a snapshot by way of a table including literature citations and also discuss these applications in more detail throughout.
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Microfluidic Systems with Ion-Selective Membranes
Vol. 7 (2014), pp. 317–335More LessWhen integrated into microfluidic chips, ion-selective nanoporous polymer and solid-state membranes can be used for on-chip pumping, pH actuation, analyte concentration, molecular separation, reactive mixing, and molecular sensing. They offer numerous functionalities and are hence superior to paper-based devices for point-of-care biochips, with only slightly more investment in fabrication and material costs required. In this review, we first discuss the fundamentals of several nonequilibrium ion current phenomena associated with ion-selective membranes, many of them revealed by studies with fabricated single nanochannels/nanopores. We then focus on how the plethora of phenomena has been applied for transport, separation, concentration, and detection of biomolecules on biochips.
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Solid-Phase Biological Assays for Drug Discovery
Vol. 7 (2014), pp. 337–359More LessIn the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.
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Resonance-Enhanced Multiphoton Ionization Mass Spectrometry (REMPI-MS): Applications for Process Analysis
Vol. 7 (2014), pp. 361–381More LessProcess analysis is an emerging discipline in analytical sciences that poses special requirements on analytical techniques, especially when conducted in an online manner. Mass spectrometric methods seem exceedingly suitable for this task, particularly if a soft ionization method is applied. Resonance-enhanced multiphoton ionization (REMPI) in combination with time-of-flight mass spectrometry (TOFMS) provides a selective and sensitive means for monitoring (poly)aromatic compounds in process flows. The properties of REMPI and various variations of the ionization process are presented. The potential of REMPI for process analysis is highlighted with several examples, and drawbacks of the method are also noted. Applications of REMPI-TOFMS for the detection and monitoring of aromatic species in a large variety of combustion processes comprising flames, vehicle exhaust, and incinerators are discussed. New trends in technical development and combination with other analytical methods are brought forward.
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Nanoscale Methods for Single-Molecule Electrochemistry
Vol. 7 (2014), pp. 383–404More LessThe development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.
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Nucleic Acid Aptamers for Living Cell Analysis
Vol. 7 (2014), pp. 405–426More LessCells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as “chemical antibodies,” have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.
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High-Throughput Proteomics
Vol. 7 (2014), pp. 427–454More LessMass spectrometry (MS)–based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
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