Proteomics: technology development and applications

Technology development in, and the application of, proteomics are emerging areas among chemical engineers and others who presented at the 2008 American Institute of Chemical Engineers (AIChE) Annual Meeting. Overall, the centennial meeting offered a broad current perspective on the discipline of chemical engineering as it enters its second century. Biomedical and biochemical engineering continue to grow as important facets of the discipline. Within these, the value and applicability of proteomics were demonstrated in a number of interesting presentations. This year, as in the recent past, the AIChE Annual Meeting was held in conjunction with the American Electrophoresis Society Annual Meeting. American Electrophoresis Society presenters offered further academic and industrial viewpoints on the still-developing role of proteomics and proteomic technologies in biological and clinical analyses.     

Proteomics: Current technologies and applications in neurological disorders and toxicology

Summary. Proteomics is the science that studies the proteins in general and in particular their changes, resulting from various disorders or the effect of external factors, such as toxic agents. It has as goal the detection of novel drug targets, diagnostic markers and the investigation of biological events. Proteomics has emerged the last few years and its major difference from the previously existing protein analytical techniques is that it does not analyze the proteins one by one, but in a possibly automated, large-scale mode. In this article, the state of the art of proteomics in our laboratory is presented, as well as selected applications of proteomics in the study of disorders of the central nervous system and of toxic events. Received March 5, 2001 Accepted September 13, 2001     

Proteomics applied to exercise physiology: a cutting-edge technology

Exercise research has always drawn the attention of the scientific community because it can be widely applied to sport training, health improvement, and disease prevention. For many years numerous tools have been used to investigate the several physiological adaptations induced by exercise stimuli. Nowadays a closer look at the molecular mechanisms underlying metabolic pathways and muscular and cardiovascular adaptation to exercise are among the new trends in exercise physiology research. Considering this, to further understand these adaptations as well as pathology attenuation by exercise, several studies have been conducted using molecular investigations, and this trend looks set to continue. Through enormous biotechnological advances, proteomic tools have facilitated protein analysis within complex biological samples such as plasma and tissue, commonly used in exercise research. Until now, classic proteomic tools such as one- and two-dimensional polyacrylamide gel electrophoresis have been used as standard approaches to investigate proteome modulation by exercise. Furthermore, other recently developed in gel tools such as differential gel electrophoresis (DIGE) and gel-free techniques such as the protein labeling methods (ICAT, SILAC, and iTRAQ) have empowered proteomic quantitative analysis, which may successfully benefit exercise proteomic research. However, despite the three decades of 2-DE development, neither classic nor novel proteomic tools have been convincingly explored by exercise researchers. To this end, this review gives an overview of the directions in which exercise-proteome research is moving and examines the main tools that can be used as a novel strategy in exercise physiology investigation.     

Proteomics technologies and challenges

Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.     

Proteomics technologies in endometriosis

Endometriosis is a common disorder that is associated with infertility and pelvic pain. Diagnosis is based on the visualization of endometriotic lesions during surgery as no reliable serum marker is currently available. The etiology of endometriosis is largely unknown. Over the last 20 years, several proteomics technologies have been used to research novel proteins with a potential etiological role in endometriosis, and to identify candidate serum markers for this condition. While some molecules identified by proteomics technologies may have a relevant role in the pathogenesis of endometriosis, the research of potential serum markers for this condition is still far from any clinical application. This review summarizes the state of the art and potential applications of proteomics in endometriosis research.     

Proteomics and physiology of erythritol-producing strains

In-depth knowledge bases on physiological properties of microbes are required to design a better microbial system at a gene level and to develop an industrially viable process in an optimized scheme. Proteomic analyses of industrially useful microorganisms are particularly important for achieving such objectives. In this review, industrial application of erythritol in food and pharmaceutical areas and proteomic techniques for erythritol-producing microbes were presented. Proteomic technologies for erythritol-producing strains such as Candida magnoliae contained protein or peptide sample preparation for two-dimensional electrophoresis and mass spectrometry, analysis of proteome with matrix assisted laser desorption-ionization/time-of-flight mass spectrometry, liquid chromatography/electrospray ionization/tandem mass spectrometry and similarity searching algorithms. The proteomic information was applied to predict the carbon metabolism of erythritol-synthesizing microorganisms.     

Proteomics: Concepts and applications in human medicine

Proteomics is the complete evaluation of the function and structure of proteins to understand an organism’s nature. Mass spectrometry is an essential tool that is used for profiling proteins in the cell. However, biomarker discovery remains the major challenge of proteomics because of their complexity and dynamicity. Therefore, combining the proteomics approach with genomics and bioinformatics will provide an understanding of the information of biological systems and their disease alteration. However, most studies have investigated a small part of the proteins in the blood. This review highlights the types of proteomics, the available proteomic techniques, and their applications in different research fields.     

Proteomics: applications in basic and applied biology

The rapid evolution of proteomics has continued during the past year, with a series of innovations in the core technologies of two-dimensional electrophoresis and mass spectrometry, and a diversity of productive research programmes. Well-annotated proteomics databases are now emerging in a number of fields to provide a platform for systematic research, with particularly promising progress in clinical applications such as cardiology and oncology. Large-scale quantitative research, comparable in power and sensitivity to that achieved for gene expression, is thus becoming a reality at the protein level.     

Cutting-edge technology. I. Global gene expression profiling using DNA microarrays

Having the complete human genomic sequence poses a new challenge: to use genomic structural information to display and analyze biological processes on a genome-wide scale to assign gene function. DNA microarrays are a miniaturized, ordered arrangement of nucleic acid fragments from individual genes located at defined positions on a solid support, enabling the analysis of thousands of genes in parallel by specific hybridization. This review describes technical aspects, discusses relevant applications, and suggests factors affecting the use of this technology and how it fits in the grand scheme of meeting the needs of the postgenomic era.     

Proteomics: a link between genomics,genetics and physiology

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant biology. In the study of pleiotropic effects of mutants and in the analysis of responses to hormones and to environmental changes, the identification of involved metabolic pathways can be deduced from the function of affected proteins. In molecular quantitative genetics, proteomics can be used to map translated genes and loci controlling their expression, which can be used to identify proteins accounting for the variation of complex phenotypic traits. Linking gene expression to cell metabolism on the one hand and to genetic maps on the other, proteomics is a central tool for functional genomics.     

Cutting-edge technology: IV. Genomic engineering for studies of the gastrointestinal tract in mice

Advances in our understanding of the complex, dynamic interactions that exist among the gastrointestinal microflora, the epithelium of the gastrointestinal mucosae, and the immune system have been facilitated by powerful new genetic tools. Recent understanding that the gastrointestinal epithelium performs not only a barrier function but is also an active sensor of the microflora and an important intermediary in regulating and integrating cross-talk between it and cells of the innate and adaptive immune systems provides one of the most fertile and challenging areas for application of these technologies. The intestinal epithelium also represents an important model system for study of programs of cell lineage commitment and differentiation, given its continual and rapid regeneration throughout life and the regional differences in these programs that exist along the gastrocolonic and crypt-villous axes. This review will highlight current and emerging technologies that are available in the mouse model for identification and manipulation of genetic elements that regulate the normal and pathological physiology of the intestinal tissues in the post-genomic era.     

Proteomics for biodefense applications: progress and opportunities

The increasing threat of bioterrorism and continued emergence of new infectious diseases has driven a major resurgence in biomedical research efforts to develop improved treatments, diagnostics and vaccines, as well as increase the fundamental understanding of the host immune response to infectious agents. The availability of multiple mass spectrometry platforms combined with multidimensional separation technologies and microbial genomic databases provides an unprecedented opportunity to develop these much needed resources. An overview of current proteomic strategies applied to microbes and viruses considered potential bioterrorism agents is presented. The emerging area of immunoproteomics as applied to the development of new vaccine targets is also summarized. These powerful research approaches can generate a multitude of potential new protein targets; however, translating these proteomic discoveries to useful counter-bioterrorism products will require large collaborative research efforts across multiple basic science and clinical disciplines. A translational proteomic research paradigm illustrating this approach using influenza virus as an example is discussed.     

Proteomics for biodefense applications: progress and opportunities

The increasing threat of bioterrorism and continued emergence of new infectious diseases has driven a major resurgence in biomedical research efforts to develop improved treatments, diagnostics and vaccines, as well as increase the fundamental understanding of the host immune response to infectious agents. The availability of multiple mass spectrometry platforms combined with multidimensional separation technologies and microbial genomic databases provides an unprecedented opportunity to develop these much needed resources. An overview of current proteomic strategies applied to microbes and viruses considered potential bioterrorism agents is presented. The emerging area of immunoproteomics as applied to the development of new vaccine targets is also summarized. These powerful research approaches can generate a multitude of potential new protein targets; however, translating these proteomic discoveries to useful counter-bioterrorism products will require large collaborative research efforts across multiple basic science and clinical disciplines. A translational proteomic research paradigm illustrating this approach using influenza virus as an example is discussed.