Qualitative and quantitative evaluation of Simon™, a new CE-based automated Western blot system as applied to vaccine development

Many CE-based technologies such as imaged capillary IEF, CE-SDS, CZE, and MEKC are well established for analyzing proteins, viruses, or other biomolecules such as polysaccharides. For example, imaged capillary isoelectric focusing (charge-based protein separation) and CE-SDS (size-based protein separation) are standard replacement methods in biopharmaceutical industries for tedious and labor intensive IEF and SDS-PAGE methods, respectively. Another important analytical tool for protein characterization is a Western blot, where after size-based separation in SDS-PAGE the proteins are transferred to a membrane and blotted with specific monoclonal or polyclonal antibodies. Western blotting analysis is applied in many areas such as biomarker research, therapeutic target identification, and vaccine development. Currently, the procedure is very manual, laborious, and time consuming. Here, we evaluate a new technology called Simple Western? (or Simon?) for performing automated Western analysis. This new technology is based on CE-SDS where the separated proteins are attached to the wall of capillary by a proprietary photo activated chemical crosslink. Subsequent blotting is done automatically by incubating and washing the capillary with primary and secondary antibodies conjugated with horseradish peroxidase and detected with chemiluminescence. Typically, Western blots are not quantitative, hence we also evaluated the quantitative aspect of this new technology. We demonstrate that Simon? can quantitate specific components in one of our vaccine candidates and it provides good reproducibility and intermediate precision with CV <10%.     

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.     

Advances in Biohybridized Planar Polymer Membranes and Membrane-Like Matrices

The past few decades have seen increasing growth in the field of biomimetic membranes and thus also a rapid expansion of their biomedical and technological applications. Versatility, stability and scalability have moved biohybrid polymer membranes into the limelight. This review focuses on planar, soft polymer membranes and polymer-based matrices and their role as a host for different types of biomolecules. Because biomimetic polymer platforms present an extensive, ever-growing field, we limit ourselves mostly to the discussion of producing planar polymer membranes on solid supports that lend themselves to functionalization by biomolecules. We present an overview of the major highlights and challenges associated with the biohybridization of such polymer platforms. In particular, we elaborate on procedures developed to maintain optimal peptide and membrane protein performance in a customized polymer membrane or membrane-like environment. Finally, we discuss a number of applications of such biohybridized polymer platforms and contemplate future developments to further exploit their potential.     

Microfluidic Pressure Driven Liquid Chromatography of Biologically Relevant Samples

An overview of the literature regarding the most recent and innovative developments in microfluidic devices for pressure-driven chromatographic separations is given, with a focus on proteomics and metabolomics applications. The applications can be considered as the main driving force for the developments in this research field, since they put high demands on the analytical technology such as for throughput, efficiency, and sensitivity and for the possibilities to interface with mass spectrometry. The developments are evaluated based on the feasibility for use in work flows for the analysis of biologically relevant samples. The literature up to the first half of 2011 is covered. Electrophoretic separations are not within the scope of this review. Several strategies have been described to obtain a retentive phase in microfluidic channels. Open channels with the stationary phase bound to the walls appear to be relatively easy to make. However, the retention in such channels is generally very low for separations of relevant samples. Microfabrication of perfectly ordered topographic structures is the most innovative of the methods discussed for the creation of stationary phases in narrow channels. Several groups work on the improvement of the surface-to-volume ratio in such channels, using different methods, and the developments towards real applications are promising. Channels packed with spherical particles and in situ polymerized monoliths for pressure-driven separations are the most frequently applied. Microfluidic devices with an integrated injection system, a (packed) separation column and a spray tip for coupling to a mass spectrometer are already commercially available, and used in practice in proteomics and metabolomics. Finally, the inherent advantages of microfluidic devices for multidimensional separations have been shown in practice in a number of studies. In these studies, pressure-driven chromatography is coupled (in series or multiplexed) to an electrophoretic separation method. The high peak capacity of such 2-dimensional separations has been shown.

     

Some recent developments in reference methodology within the United Kingdom

 The UK Valid Analytical Measurement Programme has pump-primed developments in chemical metrology, through a major project on reference methodology and reference materials. This paper provides an overview of developments during 1994–1997 and covers work on primary methods for trace inorganic and trace organic analysis, including the use of isotope dilution mass spectrometry; studies of sample pre-treatment, including digestion, extraction, and separation aimed at improving this weak link in the traceability chain; prioritisation, production and marketing of both pure substance and matrix reference materials; and international collaboration concerned with interlaboratory comparisons and the development of concepts, terminology and systems to underpin the international chemical measurement system. References are given to a number of papers covering specific parts of the programme. Received: 5 August 1998 · Accepted: 12 September 1998     

Capillary electrochromatography of peptides and proteins

This paper reviews recent progress in bioanalysis using capillary electrochromatography (CEC), especially in the field of separation of proteins and peptides. Fundamentals of CEC are briefly discussed. Since most of the recent developments on CEC have focused on column technology, i.e., design of new stationary phases and development of new column configurations, we describe here a variety of column architectures along with their advantages and disadvantages. Newly emerged column technologies in CEC for high speed and high efficiency separation are also discussed. Different analytical platforms of CEC such as pressure-assisted CEC or voltage-assisted micro- high-performance liquid chromatography (HPLC), CEC with different detection techniques, CEC on microchip platforms and multidimensional electrochromatography with their applications in peptide and protein analysis are presented.     

Direct Blue 71 staining as a destaining‐free alternative loading control method for Western blotting

In Western blotting, a suitable loading control is indispensable for correcting errors in the total amount of loaded protein. Immunodetection of housekeeping proteins and total protein staining have traditionally been used as loading control methods. Direct Blue 71 (DB71) staining—a novel, sensitive, dye‐binding staining method compatible with immunodetection—may offer advantages over these traditional loading control methods. Three common neuroscientific samples (human plasma, human oligodendrocytes, and rat brain) were employed to assess DB71 staining as a loading control method for Western blotting. DB71, CBB, one traditional housekeeping protein, and one protein of interest were comparatively assessed for reliability and repeatability and linear dynamic range over 2.5–40 μg of protein loaded. DB71's effect on the reliability and repeatability and linear dynamic range of immunoreaction were also assessed. Across all three sample types, DB71 was either equivalent or superior to CBB and housekeeping protein‐based methods in terms of reliability and repeatability and linear dynamic range. Across all three sample types, DB71 staining did not impair the reliability and repeatability or linear dynamic range of immunoreaction. Our results demonstrate that the DB71 staining can be used as a destaining‐free alternative loading control method for Western blotting.     

Microfluidic approaches for cancer cell detection, characterization, and separation

This article reviews the recent developments in microfluidic technologies for in vitro cancer diagnosis. We summarize the working principles and experimental results of key microfluidic platforms for cancer cell detection, characterization, and separation based on cell-affinity micro-chromatography, magnetic activated micro-sorting, and cellular biophysics (e.g., cell size and mechanical and electrical properties). We examine the advantages and limitations of each technique and discuss future research opportunities for improving device throughput and purity, and for enabling on-chip analysis of captured cancer cells.     

Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes

In plasma membrane proteome research, contamination of the isolated plasma membrane fraction with proteins from other organelles is still a problem. Even if highly specific isolation methods are used, such as density gradient centrifugation combined with selective extraction, contaminating proteins cannot be completely removed. To solve this problem, a protocol for the isolation of highly pure plasma membrane fractions from rat liver and two different hepatocellular carcinoma cell lines was developed. Magnetic beads with immobilized mAb's against highly expressed membrane proteins were used for specific binding of membrane vesicles and their separation from other organelles. Isolated plasma membranes were further selectively solubilized with different reagents and analyzed by use of different methods, such as Western blotting, 1- and 2-DE, and MS. Purification and further selective solubilization was validated by use of mAb's against the marker integral plasma membrane protein carcinoembryonic antigen cell adhesion molecule 1, and identification of isolated proteins by MS. The method presented here minimizes contamination with other organelles and enables further identification of membrane proteins.     

Multistrip Western blotting to increase quantitative data output

The qualitative and quantitative measurements of protein abundance and protein modification states are essential in understanding their role in diverse cellular processes. Traditional Western blotting technique, though sensitive, is prone to produce substantial errors and is not readily adapted to high-throughput technologies. We propose a modified immunoblotting procedure, which is based on simultaneous transfer of proteins from multiple gel-strips onto the same membrane, and is compatible with any conventional gel electrophoresis system. As a result, the data output per single blotting cycle can readily be increased up to ten-fold. In contrast to the traditional "one protein detection per electrophoresis cycle", this procedure allows simultaneous monitoring of up to nine different proteins. In addition to maintaining the ability to detect picogram quantities of protein, the modified system substantially improves data accuracy by reducing signal errors by two-fold. Multistrip Western blotting procedure allows making statistically reliable side-by-side comparisons of different or repeated sets of data. Compared to the traditional methods, this approach provides a more economical, reproducible, and effective procedure, facilitating the generation of large amounts of high-quality quantifiable data.     

Detection of carbohydrates in capillary electrophoresis

This review focuses on recent developments in sensitive detection modes for carbohydrates after separation by capillary electrophoretic methods. To bring detection sensitivity for carbohydrates analysis in line with current methods in protein sequencing, concentration detection limits of 10⁻⁶ molar or better are requires. A discussion of mass detection limits and concentration detection limits is followed by an overview of detection modes for natural and labeled carbohydrates. Amperometric detection and UV and laser-induced fluorescence detection after reductive amination, in particular with 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS), are discussed in more detail. Finally, the paper outlines developments to be expected in the near future, focusing on the needs in glycobiology such as improved sensitivity and selectivity.     

Computational Methods for MOF/Polymer Membranes

Metal–organic framework (MOF)/polymer mixed matrix membranes (MMMs) have received significant interest in the last decade. MOFs are incorporated into polymers to make MMMs that exhibit improved gas permeability and selectivity compared with pure polymer membranes. The fundamental challenge in this area is to choose the appropriate MOF/polymer combinations for a gas separation of interest. Even if a single polymer is considered, there are thousands of MOFs that could potentially be used as fillers in MMMs. As a result, there has been a large demand for computational studies that can accurately predict the gas separation performance of MOF/polymer MMMs prior to experiments. We have developed computational approaches to assess gas separation potentials of MOF/polymer MMMs and used them to identify the most promising MOF/polymer pairs. In this Personal Account, we aim to provide a critical overview of current computational methods for modeling MOF/polymer MMMs. We give our perspective on the background, successes, and failures that led to developments in this area and discuss the opportunities and challenges of using computational methods for MOF/polymer MMMs.     

Wavefunction-based electron correlation methods for solids

In this article we provide an overview of the most common ways of treating electron correlation effects in 3D-periodic systems with some emphasize on wavefunction-based correlation methods such as the method of increments and the local MP2 method implemented in the Cryscor program. We discuss strengths and weaknesses of the different approaches and give examples for their application. Additionally, for the method of increments we discuss recent developments for its application to open shell systems and problems related to the treatment of graphene sheets.     

Advanced Immobilization and Amplification for High Performance Protein Chips

With the success of high-throughput DNA microarrays, protein biochips have been intensively investigated and broadly used in bioscience research, clinic diagnosis, drug discovery, and other applications. However, there is great need to significantly improve the sensitivity of protein chips, especially in early diagnosis. A major challenge of improving sensitivity is that protein detection does not have an effective amplification method, such as PCR for DNA microarrays. Construction of unique biofilms for efficient immobilization of protein probes and innovation of new amplification schemes could play a critical role in performance improvement of protein biochips. With dramatic developments in microfabrication, nanotechnologies, and biotechnologies, enormous progress has been made, particularly in improving biosensing sensitivity. This article reviews new advances in protein biochip technologies with emphasis on novel approaches for efficient probe immobilization and nanomaterials-assisted signal amplification for high performance protein chips. Prominent progress in integration of protein microarrays with microfluidic platforms is briefly discussed. The major challenges and perspectives on the future of protein biochips are also addressed.     

Per Aqueous Liquid Chromatography (PALC) as a Simple Method for Native Separation of Protein A

Staphylococcal protein A (protein A) is an important protein frequently used in research studies within the fields of biomedicine and biotechnology. Due to some limitations in available protein purification methods which can hold the native structure of the protein A without changing the folding or adding histidine to structure of this protein, its separation in the native form is difficult. In this study, a new cost-effective and powerful technique was introduced for separation of the full-length and truncated forms of recombinant protein A, without any alteration in their 3D structures. Per aqueous liquid chromatography with bare silica gel stationary phase and water:acetonitrile as the mobile phase was proved to be an attractive choice among the range of separation methods. Similar to hydrophilic liquid chromatography, this method employs high percentage of water in mobile phase. The effects of mobile phase composition, pH, and salt concentration on the retention behavior of protein A on bare silica gel stationary phases were investigated. In this method, applying high amounts of aqueous solvent accompanied by a minimum percentage of organic solvent could successfully separate protein A with preservation of folding, and any affinity-tagged group such as histidine has not occurred on its structure. Purity of the fractions obtained by the proposed method was confirmed using SDS-PAGE, western blotting, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. According to the results of ELISA, separated proteins retained their ability of binding to antibody.     

Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies

Chromatographic method has long been recognized as the most widely used separation method in bioanalytical research. However, the relatively low sensitivity of existing chromatographic methods remains a significant challenge, as the requirements for experimental procedures become more demanding. This review discusses the main causes for the low sensitivity of chromatographic methods and aims to introduce different technologies for enhancing their sensitivity in the following aspects: (i) different pretreatment methods for improving clean-up efficiency and recovery; (ii) derivatization step for altering the chromatographic behavior of analytes and enhancing MS ionization efficiency; (iii) optimal LC–MS conditions and appropriate separation mechanism; and (iv) applications of other chromatographic methods, including miniaturized LC, 2D-LC, 2D-GC, and supercritical fluid chromatography. Altogether, this review is devoted to summarizing the recent technologies reported in the literature and providing new strategies for the detection of bioanalytes.     

Capillary electrophoresis-mass spectrometry for the analysis of intact proteins 2007-2010

CE coupled to MS has proven to be a powerful analytical tool for the characterization of intact proteins, as it combines the high separation efficiency of CE with the selectivity of MS. This review provides an overview of the development and application of CE-MS methods within the field of intact protein analysis as published between January 2007 and June 2010. Ongoing technological developments with respect to CE-MS interfacing, capillary coatings for CE-MS, coupling of CIEF with MS and chip-based CE-MS are treated. Furthermore, CE-MS of intact proteins involving ESI, MALDI and ICP ionization is outlined and overviews of the use of the various CE-MS methods are provided by tables. Representative examples illustrate the applicability of CE-MS for the characterization of proteins, including glycoproteins, biopharmaceuticals, protein-ligand complexes, biomarkers and dietary proteins. It is concluded that CE-MS is a valuable technique with high potential for intact protein analysis, providing useful information on protein identity and purity, including modifications and degradation products.     

Chromatographic determination of pesticides in soil: Current trends in analysis and sample preparation

Soil is a primary sink and reservoir for pesticides pollution and one of the priority objects in terms of pesticides safety guidelines. Pesticides’ analysis in soil is a field of research which is in constant development facing numerous challenges such as the increasing amount and variety of analytes and their combinations, as well as the increasing demand for faster, simpler, more accurate and multiresidue analysis. This review provides the summary of studies on pesticides analysis in soil based on chromatography-coupled methods published between 2015 and 2022. We discuss the shift toward faster, greener, and simpler alternatives to conventional techniques, application of sample preparation and detection methods to targeted and untargeted pesticide analysis, as well as the developments in stereoselective determination of chiral pesticides. The sample preparation methods such as solid-phase extraction, dispersive solid-phase extraction, and derived methods, as well as the recent trends and developments in chromatographic separation of pesticides are covered in this review. For sample preparation, the QuEChERS method is replacing other techniques and has proved to be efficient in both screening and accurate quantification in multiresidue analysis. Shift towards minimal sample preparation is supported by a wider application of highly sensitive and selective separation and detection systems such as LC-MS/MS. The features of different methods of sample preparation and detection are discussed with focus on optimal parameters, advantages, and drawbacks. The optimal parameters of sample preparation methods were summarized based on respective publications, which makes the review a useful tool for method development and further investigations.     

Advances in capillary electrophoresis: the challenges to liquid chromatography and conventional electrophoresis

In the 1980s, capillary electrophoresis (CE) developed rapidly into a first-class analytical separation technique. Its advances in instrumentation and method development will not only enhance or complement existing mature separation techniques such as liquid chromatography and conventional slab gel electrophoresis, but will also severely challenge these separation methods. A brief overview of the most striking achievements of CE in the 1980s is given. which illustrates the challenges to liquid chromatography and conventional slab gel electrophoresis, and some detailed discussions are presented to highlight the advantages of CE. New developments in CE that can be expected for the 1990s include especially column technology, separation chemistry and instrumentation, which will serve further to diversify and improve the applicability of this technique in areas which are poorly addressed by other separation methods. This paper considers and speculates on the technological advancements that can be expected to emerge for CE in the 1990s.     

Porous metal-organic frameworks as platforms for functional applications

Metal-organic frameworks (MOFs), also known as coordination polymers, have emerged as a new class of crystalline porous materials, which are constructed from metal ions or metal ion clusters and bridging organic linkers. MOFs have tunable pores and functionalities, and usually exhibit very high surface areas. The potential applications of porous MOFs cover a broad range of fields and most of their applications are related to pore sizes, shapes and structures/environments. In this feature article, we provide an overview of the recent developments of porous MOFs as platforms in the functional applications of sorption and separation, heterogeneous catalysis, as supports/host matrices for metal nanoparticles, and as templates/nanoreactors for new material preparation.