Advances in mass spectrometry-based post-column bioaffinity profiling of mixtures

In the screening of complex mixtures, for example combinatorial libraries, natural extracts, and metabolic incubations, different approaches are used for integrated bioaffinity screening. Four major strategies can be used for screening of bioactive mixtures for protein targets—pre-column and post-column off-line, at-line, and on-line strategies. The focus of this review is on recent developments in post-column on-line screening, and the role of mass spectrometry (MS) in these systems. On-line screening systems integrate separation sciences, mass spectrometry, and biochemical methodology, enabling screening for active compounds in complex mixtures. There are three main variants of on-line MS based bioassays: the mass spectrometer is used for ligand identification only; the mass spectrometer is used for both ligand identification and bioassay readout; or MS detection is conducted in parallel with at-line microfractionation with off-line bioaffinity analysis. On the basis of the different fields of application of on-line screening, the principles are explained and their usefulness in the different fields of drug research is critically evaluated. Furthermore, off-line screening is discussed briefly with the on-line and at-line approaches.     

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term “catalomics” defines an emerging ‘-omics’ field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.     

Mass spectrometry of the human pituitary proteome: identification of selected proteins

The field of proteomics involves the combined application of advanced separation techniques, mass spectrometry, and bioinformatics tools to characterize proteins in complex biological mixtures. Here we report the identification of nine proteins from the human pituitary proteome, using the proteomics approach. The pituitary proteins were separated by two-dimensional electrophoresis, and were visualized by silver staining. The proteins of interest were subjected to in-gel digestion with trypsin, and the masses of the resulting peptides were determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This tryptic mass map was used to identify the proteins through a search of a protein-sequence database. The identified proteins include important hormones, and enzymes with various catalytic activities. These proteins will be used to construct a two-dimensional reference database of the human pituitary. This database will be employed to study changes in the pituitary proteome that are associated with the formation of pituitary tumors.     

Organoiodine complexes: Structural and functional variety

The present review summarizes the results of structural studies of organoiodine complexes. Particular emphasis is given to the role of intermolecular interactions such as halogen—halogen (I…I), hydrophobic, fy—fy stacking, and hydrogen bonds (C—H…I) in the formation of supramolecular iodine-containing architectures. The molecular formula, size, shape, and stability of the polyhalide ion and the way of its coordination by an outer-sphere cation or an organic macromolecule depend on the nature and symmetry of the cationic environment, the ability of a solvating solvent to form complexes with iodine, and the conditions of the synthesis. Efforts have been made to highlight a structural and functional variety of iodine-containing complexes and estimate the prospects of using them as organic conductors, magnetic materials, liquid electrolytes, and biologically active compounds.     

Multi-dimensional liquid chromatography in proteomics—A review

Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.     

Approaches to bioresponse-linked instrumental analysis in water analysis

A new concept based on hyphenation of biotests, for biological selection, and chemical analysis is introduced for water analysis. Biomolecular recognition components such as receptors, enzymes, and nucleic acids integrated in biological reaction chains are used for binding and selective enrichment of known and unknown biologically active substances in water samples; this is followed by identification and quantitation. The coupling of biomolecular recognition and binding to chemical analysis can be achieved either in discrete analytical steps, e.g. binding and elution of bioactive ligands from affinity columns followed by chemical analysis, or by methods capable of monitoring the binding of the ligand and simultaneous verification of its identity. This analytical strategy, denoted bioresponse-linked instrumental analysis (BLIA), enables detection of potential biological effects and identification of the analyte causing these effects. Several examples are presented.     

New perspectives in multireference perturbation theory: the n-electron valence state approach

The n-electron valence state perturbation theory (NEVPT) is a form of multireference perturbation theory which is based on a zero order reference wavefunction of CAS-CI type (complete active space configuration interaction) and which is characterized by the utilization of correction functions (zero order wavefunctions external to the CAS) of multireference nature, obtained through the diagonalization of a suitable two-electron model Hamiltonian (Dyall’s Hamiltonian) in some well defined determinant spaces. A review of the NEVPT approach is presented, starting from the original second order state-specific formulation, going through the quasidegenerate multi-state extension and arriving at the recent implementations of the third order in the energy and of the internally contracted configuration interaction. The chief properties of NEVPT—size consistence and absence of intruder states—are analyzed. Finally, an application concerning the calculation of the vertical spectrum of the biologically important free base porphin molecule, is presented.     

Playing tag with quantitative proteomics

There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review, we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative proteomics using stable isotope labeling and their applications to current insightful biological inquiries. Figure Chemical modules of isotopic tags for quantitative proteomics.     

Application of Mass Spectrometry and Chromatography–Mass Spectrometry in Drug Analysis

The review is devoted to the use of mass spectrometry and chromatography–mass spectrometry in various areas of pharmaceutical chemistry. The role of the above techniques in the structural identification of impurities in drug preparations and in the determination of the biotransformation behavior of pharmaceuticals in human and animal bodies is shown. The inactivation of drugs under the action of external factors (oxidation by atmospheric oxygen and the effects of moisture, heat, and light) is illustrated. The use of various ionization techniques and the spectra of metastable ions for determining the structures of components of biologically active substances are exemplified.     

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by “in-gel digestion” has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches. Figure Classical in-gel digestion process for a protein band stained with CBB. Protein bands are cut from the polyacrylamide gel (1). CBB molecules (blue circles) bound to the protein are released by iterative incubation in a buffered organic solvent system (2). To increase digestion efficiency and sequence coverage proteins are reduced (3) and alkylated (4). Proteins are subsequently digested with proteolytic enzymes (scissors symbols), typically trypsin (5). Trypsin cleaves at the amino acid residues arginine (R) and lysine (K). The resulting peptides (A, B, and C) are extracted from the polyacrylamide matrix (6). The peptide solution can be further purified for analysis by mass spectrometry (Section “Concentration and desalting of peptides”)     

Current trends in isolation, separation, determination and identification of isoflavones: a review

Isoflavones are natural substances which elicit a number of physiological effects in living organisms. The substances are synthesized in plant tissues as protective agents against biotic stress (i. e. bacterial infection). Isoflavones are also an important dietary constituent in human nutrition. Modern trends in studies of isoflavones in plant materials and foodstuffs and procedures for chemical analyses of isoflavones in human body fluids and plant tissues are discussed in this review. Highly effective extraction and purification techniques, i. e. solid-phase extraction, accelerated-solvent extraction, and Soxhlet extraction, are presented. Latest procedures in chromatographic separation of isoflavones that apply different types of sorbents are described. Immunochemical analysis, electrochemical sensing of isoflavones, and spectrometric and other analytical techniques and their applications are also mentioned. Special attention is paid to the highly selective and sensitive technique of mass spectrometry and its application for identification of isoflavones and their glucosides in plants. Studies of interactions of isoflavones with cell receptors and a number of biologically active substances such as DNA and proteins are described. The review does not intend to give a complete overview of the topics considered but rather to present modern and most recent methods used in studies of isoflavones.     

Microarray: a versatile platform for high-throughput functional proteomics

The advent of microarray technologies has dramatically accelerated the functional study of proteins, including enzymes (catalomics) in a proteome. Herein, we review recent advances and exciting new developments of microarrays in high-throughput functional proteomics.     

Chromatographic Techniques for the Separation of Peptides: Application to Proteomics

The greatest challenge for proteomics is the inherently complex nature of cellular proteomes as they are highly dynamic entities. High performance liquid chromatography is an indispensable tool in proteomics research, providing high-speed, high sensitivity separation and good resolution of proteins and peptides. Chromatographic sciences have played an animated, bustling and critical role in many fields, the next challenging analytical project for the chromatographic scientists is in the area of proteomics. Which type of analysis best determines the optimal separation technique for any proteomic study? The aim of this review is to outline the different chromatographic strategies that have been employed for analysis of complex mixtures of proteins/peptides, highlighting the role of liquid chromatography coupled to mass spectrometry.     

Evaluation of enzymatic activity on nanoscale polystyrene-block-polymethylmethacrylate diblock copolymer domains

Understanding structural and functional changes of polymeric surface-bound proteins is extremely important as polymers play an increasingly significant role as arrays and substrates in proteomics applications. We carried out, for the first time, quantitative activity measurements of horseradish peroxidase (HRP) enzymes immobilized selectively on the polystyrene domains of microphase-separated polystyrene-block-polymethylmethacrylate ultrathin films. The specific enzymatic activity of HRP adsorbed on the diblock copolymer surface was evaluated and compared to that of HRP in free solution. We demonstrate that the polymeric surface-bound HRP molecules maintain approximately 85% of their activity in free solution. The unique advantages of diblock copolymer templates, involving nanoscale self-assembly and largely retained protein functionality, make the spontaneously constructed enzyme nanoarrays highly suitable as proteomics substrates. Our novel assembly method of providing functional enzymes on diblock copolymer thin films can be greatly beneficial for high-throughput and high-density protein assays.     

Secretome of the preimplantation human embryo by bottom-up label-free proteomics

A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding culture medium. The selective monitoring of these possible secretome biomarkers could make viable procedures using single-embryo transfer.     

The role of liquid chromatography in proteomics

Proteomics represents a significant challenge to separation scientists because of the diversity and complexity of proteins and peptides present in biological systems. Mass spectrometry as the central enabling technology in proteomics allows detection and identification of thousands of proteins and peptides in a single experiment. Liquid chromatography is recognized as an indispensable tool in proteomics research since it provides high-speed, high-resolution and high-sensitivity separation of macromolecules. In addition, the unique features of chromatography enable the detection of low-abundance species such as post-translationally modified proteins. Components such as phosphorylated proteins are often present in complex mixtures at vanishingly small concentrations. New chromatographic methods are needed to solve these analytical challenges, which are clearly formidable, but not insurmountable. This review covers recent advances in liquid chromatography, as it has impacted the area of proteomics. The future prospects for emerging chromatographic technologies such as monolithic capillary columns, high temperature chromatography and capillary electrochromatography are discussed.     

Coupling HPLC to on-line, post-column (bio)chemical assays for high-resolution screening of bioactive compounds from complex mixtures

It is challenging to screen and identify bioactive compounds from complex mixtures. We review a recently developed technique that couples high-performance liquid chromatography (HPLC) to on-line, post-column (bio)chemical assays and parallel chemical analysis to screen and identify bioactive compounds from complex mixtures without the need for cumbersome purification and subsequent screening. In this system, HPLC separates complex mixtures and a post-column (bio)chemical assay determines the activity of the individual compounds present in the mixtures. Parallel chemical-detection methods (e.g., diode-array detection, mass spectrometry and nuclear magnetic resonance) identify and quantify the active compounds simultaneously. We focus on relatively widely used on-line, post-column assays for antioxidant screening and less widely used hyphenated systems involving assays based on enzymes and receptors. These strategies have proved to be very useful for rapid profiling and identification of individual active components in mixtures to provide a powerful method for natural product-based drug discovery.     

Combined use of ESI–QqTOF-MS and ESI–QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs

The potential of the combined use of ESI–QqTOF-MS and ESI–QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called “match probability”, which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm—an implemented spectral purification option—enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users.     

Evaluation of two proteomics technologies used to screen the membrane proteomes of wild-type <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis> and an <Emphasis Type="SmallCaps">L</Emphasis>-lysine-producing strain

The membrane proteomes of a wild-type Corynebacterium glutamicum and an L-lysine-producing strain were quantitatively analyzed by two complementary proteomics techniques—anion exchange chromatography AIEC/SDS-PAGE and 16BAC-PAGE/SDS-PAGE—and the results were compared. Although both techniques allow for the fast screening of differences in protein abundance, AIEC/SDS-PAGE was superior to 16BAC-PAGE/SDS-PAGE with respect to protein separation, it was more suitable for relative protein quantification, and allowed more differentially regulated proteins to be detected (the succinate dehydrogenase complex, an ABC-type cobalamin/Fe³⁺ siderophore transport system, the maltose binding protein, and a subunit of the cytochrome bc-aa₃ supercomplex were upregulated, while a periplasmic component of an ABC-type transporter and an iron-regulated ABC-type transporter were downregulated in the producer). The results indicate the important role of tricarboxylic acid cycle enzymes as well as the adaptation of transport processes in L-lysine-producing cells. Since the only genetic differences between the wild type and the L-lysine producer occur between four central metabolic enzymes in the cytoplasm, our study illustrates the complex effects of metabolic engineering on cell physiology and the power of the new AIEC/SDS-PAGE proteomics approach to detect these effects.      

Overview of software options for processing,analysis and interpretation of mass spectrometric proteomic data

Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two‐dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, ‘data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it’. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large‐scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS‐based proteomics have also been speculated. Copyright © 2014 John Wiley & Sons, Ltd.