Showing papers in "Expert Review of Proteomics in 2011"
TL;DR: This article focuses on the identification of candidate cancer-associated biomarkers in carcinoma cells using state-of-the-art proteomics.
Abstract: Lipid rafts are defined as microdomains within the lipid bilayer of cellular membranes that assemble subsets of transmembrane or glycosylphosphatidylinisotol-anchored proteins and lipids (cholesterol and sphingolipids) and experimentally resist extraction in cold detergent (detergent-resistant membrane). These highly dynamic raft domains are essential in signaling processes and also form sorting platforms for targeted protein traffic. Lipid rafts are involved in protein endocytosis that occurs via caveolae or flotillin-dependent pathways. Non-constitutive protein components of rafts fluctuate dramatically in cancer with impacts on cell proliferation, signaling, protein trafficking, adhesion and apoptosis. This article focuses on the identification of candidate cancer-associated biomarkers in carcinoma cells using state-of-the-art proteomics.
257 citations
TL;DR: How HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery is summarized.
Abstract: Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule-receptor interactions, this technique has also been applied to study protein-protein complexes, such as mapping antibody-antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery.
216 citations
TL;DR: The identification of evolutionary and immunological trends may help to replace the traditional geographic- and phylogenetic-driven hypotheses for antivenom production strategies with a more rational approach based on proteome phenotype and Immunological profile similarities.
Abstract: This article covers the application of proteomic tools ('venomics', 'antivenomics' and 'venom phenotyping') to study the composition and natural history of snake venoms, and the cross-reactivity of antivenoms with homologous and heterologous venoms, to help address the neglected pathology of snake bite envenoming. The identification of evolutionary and immunological trends may help to replace the traditional geographic- and phylogenetic-driven hypotheses for antivenom production strategies with a more rational approach based on proteome phenotype and immunological profile similarities. Antivenomics and venom phenotyping may also contribute to expand the clinical range of currently existing antidotes.
162 citations
TL;DR: The scope of this article is to outline the protein microarray techniques that are currently being used for analytical and function-based proteomics and to provide a detailed analysis of the key technological advances and applications of various detection systems that are commonly used with microarrays.
Abstract: The field of proteomics has undergone rapid advancements over the last decade and protein microarrays have emerged as a promising technological platform for the challenging task of studying complex proteomes This gel-free approach has found an increasing number of applications due to its ability to rapidly and efficiently study thousands of proteins simultaneously Different protein microarrays, including capture arrays, reverse-phase arrays, tissue microarrays, lectin microarrays and cell-free expression microarrays, have emerged, which have demonstrated numerous applications for proteomics studies including biomarker discovery, protein interaction studies, enzyme-substrate profiling, immunological profiling and vaccine development, among many others The need to detect extremely low-abundance proteins in complex mixtures has provided motivation for the development of sensitive, real-time and multiplexed detection platforms Conventional label-based approaches like fluorescence, chemiluminescence and use of radioactive isotopes have witnessed substantial advancements, with techniques like quantum dots, gold nanoparticles, dye-doped nanoparticles and several bead-based methods now being employed for protein microarray studies In order to overcome the limitations posed by label-based technologies, several label-free approaches like surface plasmon resonance, carbon nanotubes and nanowires, and microcantilevers, among others, have also advanced in recent years, and these methods detect the query molecule itself The scope of this article is to outline the protein microarray techniques that are currently being used for analytical and function-based proteomics and to provide a detailed analysis of the key technological advances and applications of various detection systems that are commonly used with microarrays
150 citations
TL;DR: The accomplishments of mass spectrometry in the histone field are reviewed, and the future roadblocks that must be overcome are outlined for mass Spectrometry-based proteomics to become the method of choice for chromatin biologists.
Abstract: Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be ‘epigenetic’ or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.
122 citations
TL;DR: De novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum and many algorithms have been proposed and a selection of them are detailed in this article.
Abstract: Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field.
109 citations
TL;DR: The crucial steps needed to obtain single-cell resolution are discussed, as well as potential applications to disease research.
Abstract: Single-cell analysis is gaining popularity in the field of mass spectrometry as a method for analyzing protein and peptide content in cells. The spatial resolution of MALDI mass spectrometry (MS) imaging is by a large extent limited by the laser focal diameter and the displacement of analytes during matrix deposition. Owing to recent advancements in both laser optics and matrix deposition methods, spatial resolution on the order of a single eukaryotic cell is now achievable by MALDI MS imaging. Provided adequate instrument sensitivity, a lateral resolution of approximately 10 µm is currently attainable with commercial instruments. As a result of these advances, MALDI MS imaging is poised to become a transformative clinical technology. In this article, the crucial steps needed to obtain single-cell resolution are discussed, as well as potential applications to disease research.
96 citations
TL;DR: The main aspects of current and prospective applications of mass spectrometry and proteomic technologies to the structural characterization of gluten proteins and derived peptides are critically presented, with a focus on issues related to their detection, identification and quantification, which are relevant to the biochemical, immunological and toxicological aspects of wheat intolerance.
Abstract: Owing to its extensive use in the human diet, wheat is among the most common causes of food-related allergies and intolerances. Allergies to wheat are provoked by ingestion, inhalation or contact with either the soluble or the insoluble gluten proteins in wheat. Gluten proteins, and particularly the gliadin fraction, are also the main factor triggering celiac disease, a common enteropathy induced by ingestion of wheat gluten proteins and related prolamins from oat, rye and barley in genetically susceptible individuals. The role of gliadin and of its derived peptides in eliciting the adverse reactions in celiac disease are still far from being completely explained. Owing to its unique pathogenesis, celiac disease is widely investigated as a model immunogenetic disorder. The structural characterization of the injuring agents, the gluten proteins, assumes a particular significance in order to deepen the understanding of the events that trigger this and similar diseases at the molecular level. Recent developments in proteomics have provided an important contribution to the understanding of several basic aspects of wheat protein-related diseases. These include: the identification of gluten fractions and derived peptides involved in wheat allergy and intolerance, including celiac disease, and the elucidation of their mechanism of toxicity; the development and validation of sensitive and specific methods for detecting trace amounts of gluten proteins in gluten-free foods for intolerant patients; and the formulation of completely new substitute foods and ingredients to replace the gluten-based ones. In this article, the main aspects of current and prospective applications of mass spectrometry and proteomic technologies to the structural characterization of gluten proteins and derived peptides are critically presented, with a focus on issues related to their detection, identification and quantification, which are relevant to the biochemical, immunological and toxicological aspects of wheat intolerance.
77 citations
TL;DR: An overview of several strategies for quantitative phosphoproteomic analysis can help to elucidate signaling pathways that regulate various cellular processes is presented and discussed.
Abstract: Protein phosphorylation is a central regulatory mechanism of cell signaling pathways. This highly controlled biochemical process is involved in most cellular functions, and defects in protein kinases and phosphatases have been implicated in many diseases, highlighting the importance of understanding phosphorylation-mediated signaling networks. However, phosphorylation is a transient modification, and phosphorylated proteins are often less abundant. Therefore, the large-scale identification and quantification of phosphoproteins and their phosphorylation sites under different conditions are one of the most interesting and challenging tasks in the field of proteomics. Both 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry serve as key phosphoproteomic technologies in combination with prefractionation, such as enrichment of phosphorylated proteins/peptides. Recently, new possibilities for quantitative phosphoproteomic analysis have been offered by technical advances in sample preparation, enrichment, separation, instrumentation, quantification and informatics. In this article, we present an overview of several strategies for quantitative phosphoproteomics and discuss how phosphoproteomic analysis can help to elucidate signaling pathways that regulate various cellular processes.
74 citations
TL;DR: Recent pioneering work investigating the effects of exercise in skeletal and cardiac muscle that has uncovered novel mechanisms underlying the benefits of physical activity are highlighted.
Abstract: Regular exercise is effective in the prevention of chronic diseases and confers a lower risk of death in individuals displaying risk factors such as hypertension and dyslipidemia. Thus, knowledge of the molecular responses to exercise provides a valuable contrast for interpreting investigations of disease and can highlight novel therapeutic targets. While exercise is an everyday experience and can be conceptualized in simple terms, it is also a complex physiological phenomenon and investigation of exercise responses requires sophisticated analytical techniques and careful standardization of the exercise stimulus. Proteomic investigation of exercise is in its infancy but the ability to link changes in function with comprehensive changes in protein expression and post-translational modification holds great promise for advancing physiology. This article highlights recent pioneering work investigating the effects of exercise in skeletal and cardiac muscle that has uncovered novel mechanisms underlying the benefits of physical activity.
62 citations
TL;DR: In this paper, the authors outline considerations of reducing sample complexity by strategies such as multidimensional separations (gel-based and chromatography-based, including multi-dimensional protein identification technology).
Abstract: Measurement of biologically important effector protein molecules has been a long-standing essential component of biological research. Advances in biotechnology, in the form of high-resolution mass spectrometers, and in bioinformatics, now allow the simultaneous quantitative analysis of thousands of proteins. While these techniques still do not allow definitive identification of the entire proteome of complex mixtures, such as cells, quantitative analyses of hundreds to thousands of proteins in such complex mixtures provides a means to elucidate molecular alterations that occur during perturbation of cellular systems. This article will outline considerations of reducing sample complexity, by strategies such as multidimensional separations (gel-based and chromatography-based, including multidimensional protein identification technology). In addition, some of the most common methods used to quantitatively measure proteins in complex mixtures (2D difference in-gel electrophoresis, isotope-coded affinity tags,...
TL;DR: Current knowledge about the effects of microgravity on the proteome in different cell types are summarized and speculated, focusing on proteomic discoveries and their future potential.
Abstract: For medical and biotechnological reasons, it is important to study mammalian cells, animals, bacteria and plants exposed to simulated and real microgravity. It is necessary to detect the cellular changes that cause the medical problems often observed in astronauts, cosmonauts or animals returning from prolonged space missions. In order for in vitro tissue engineering under microgravity conditions to succeed, the features of the cell that change need to be known. In this article, we summarize current knowledge about the effects of microgravity on the proteome in different cell types. Many studies suggest that the effects of microgravity on major cell functions depend on the responding cell type. Here, we discuss and speculate how and why the proteome responds to microgravity, focusing on proteomic discoveries and their future potential.
TL;DR: The relevant technical aspects in biomarkers discovery and the course from biomarker discovery or ‘potential’ biomarkers to those that have been validated and are clinically important are summarized.
Abstract: The technology platforms for proteome analysis have advanced considerably over the last few years. Driven by these advancements in technology, the number of studies on the analysis of the proteome/peptidome, with the aim of defining clinically relevant biomarkers, has substantially risen. Urine has become an increasingly relevant target for clinically oriented proteome analysis; the first clinical trials based on urinary proteomics have been initiated, and studies including several hundred patients have been published. In this article, we summarize the relevant technical aspects in biomarkers discovery and the course from biomarker discovery or 'potential' biomarkers to those that have been validated and are clinically important. We discuss experimental design based on the statistics calculated to produce a clinically important end point. We present several examples of proteomic studies that have defined urinary biomarkers for clinical applications, focusing on capillary electrophoresis coupled to mass spectrometry as a technology. Finally, current challenges and considerations for future studies will be discussed.
TL;DR: How mass spectrometry can increase the understanding of the proteome of subcellular membranes is focused on.
Abstract: Expression of F1Fo-ATP synthase, which generates the majority of cellular ATP and is believed to be strictly confined to mitochondria, has recently been identified in ectopic locations, together with the four complexes of oxidative phosphorylation (OXPHOS) or enzymes from the Krebs cycle. Identification of these proteins has mostly been accomplished by proteomic methods and mass spectrometry - techniques that hold great promise in increasing our understanding of the proteome. The ectopic presence of ATP synthase has variably been attributed to contamination of the sample or to its action as a cell-surface receptor for apparently unrelated ligands, but OXPHOS proteins have sometimes been found to be catalytically active in oxidative phosphorylation, as they were true components of the system under investigation. The present article focuses on how mass spectrometry can increase our understanding of the proteome of subcellular membranes. We review the recent evidence for an extra-mitochondrial expression of OXPHOS by proteomics studies, highlighting what we can learn by combining these data.
TL;DR: This article illustrates how to circumvent limitations in SRM experiments on the basis of using time-scheduled chromatographic approaches and choosing appropriate spectrometric conditions, including the careful selection of the precursor and diagnostic ions.
Abstract: Selected reaction monitoring (SRM) is a highly selective and sensitive mass spectrometric methodology for precise and accurate quantification of low-abundant proteins in complex mixtures and for characterization of modified peptides, and constitutes the method of choice in targeted proteomics. Owing to its outstanding features, SRM arises as an alternative to antibody-based assays for discovery and validation of clinically relevant biomarkers, a topic that is tackled in this article. Several of the obstacles encountered in SRM experiments, mainly those derived from shared physicochemical properties of peptides (e.g., mass, charge and chromatographic retention time), can compromise selectivity and quantitation. We illustrate how to circumvent these limitations on the basis of using time-scheduled chromatographic approaches and choosing appropriate spectrometric conditions, including the careful selection of the precursor and diagnostic ions.
TL;DR: Current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.
Abstract: Proteome fractionation refers to separation at the level of intact proteins. Proteome fractionation may precede sample digestion and subsequent peptide-level separation and detection (i.e., bottom-up mass spectrometry [MS]). For top-down MS, proteome fractionation acts as a stand-alone separation platform, since intact proteins are directly analyzed by the mass spectrometer. Regardless of the MS identification strategy, separation of intact proteins has clear benefits as a result of decreasing sample complexity. However, this stage of the workflow also creates considerable challenges, which are generally absent from the counterpart peptide separation experiment. For example, maintaining protein solubility is a key concern before, during and after separation. To this end, surfactants such as sodium dodecyl sulfate may be employed during fractionation, so long as they are eliminated prior to MS. In this article, current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.
TL;DR: The advantages of mRNA display are summarized by comparing it with other widely used peptide or protein-selection techniques, and various applications of this technique in studying protein–protein interactions are discussed.
Abstract: mRNA display is a genotype-phenotype conjugation method that allows for amplification-based, iterative rounds of in vitro selection to be applied to peptides and proteins mRNA display can be used to display both long natural protein and short synthetic peptide libraries with unusually high diversities for the investigation of protein-protein interactions Here, we summarize the advantages of mRNA display by comparing it with other widely used peptide or protein-selection techniques, and discuss various applications of this technique in studying protein-protein interactions
TL;DR: Which tumor antigen-specific antibodies are prognostic biomarkers of cancer outcome, and emerging proteomic methods for the isolation and cloning of these antibodies for potential molecular diagnostics and therapeutics are reviewed.
Abstract: The development of proteomic technologies that display a wide variety of antigenic structures has led to the identification of autoantibodies to cancer-derived tumor antigens. These autoantibodies have been detected in sera from patients with multiple cancer types, and are being evaluated as biomarkers for early cancer detection. It is not known whether these antibodies also contribute to active immune surveillance or even tumorigenicity of developing tumors. Here, we review which tumor antigen-specific antibodies are prognostic biomarkers of cancer outcome, and emerging proteomic methods for the isolation and cloning of these antibodies for potential molecular diagnostics and therapeutics.
TL;DR: The substructures of some subcellular organelles, such as the cell nucleus, mitochondria and chloroplasts, have been taken into consideration by several studies in recent years and create a new research topic, namely ‘protein sub-subcellular location prediction’, which goes one level deeper than classic protein subcellULAR location prediction.
Abstract: In the last two decades, the number of the known protein sequences increased very rapidly. However, a knowledge of protein function only exists for a small portion of these sequences. Since the experimental approaches for determining protein functions are costly and time consuming, in silico methods have been introduced to bridge the gap between knowledge of protein sequences and their functions. Knowing the subcellular location of a protein is considered to be a critical step in understanding its biological functions. Many efforts have been undertaken to predict the protein subcellular locations in silico. With the accumulation of available data, the substructures of some subcellular organelles, such as the cell nucleus, mitochondria and chloroplasts, have been taken into consideration by several studies in recent years. These studies create a new research topic, namely ‘protein sub-subcellular location prediction’, which goes one level deeper than classic protein subcellular location prediction.
TL;DR: This article covers the latest contributions of proteomics to the structural and functional characterization of proteasomes and their associated proteins, but also to the detection of proteAsomes as clinical biomarkers in diseases.
Abstract: This article covers the latest contributions of proteomics to the structural and functional characterization of proteasomes and their associated proteins, but also to the detection of proteasomes as clinical biomarkers in diseases. Proteasomes are highly heterogenous supramolecular complexes and constitute important cellular proteases controlling the pool of proteins involved in key cellular functions. The comprehension of the structure/function relationship of proteasomes is therefore of major interest in biology. Numerous biochemical methods have been employed to purify proteasomes, and have led to the identification of complexes of various compositions - depending on the experimental conditions and the type of strategy used. In association with protein separation and enrichment techniques, modern mass spectrometry instruments and mass spectrometry-based quantitative methods, they have led to unprecedented breakthroughs in the in-depth analysis of the diversity and dynamics of proteasome composition and localization under various stimuli or pathological contexts. Proteasome inhibitors are now used in clinics for the treatment of cancer, and recent studies propose that the proteasome should be considered as a predictive biomarker for various pathologies.
TL;DR: The state-of-the-art in the field of cerebrospinal fluid-based NDD is presented, and some of the hypotheses of how the future development of NDD tools might look are summarized.
Abstract: Neurochemical dementia diagnostics (NDD) is a routine laboratory tool used in the diagnostic process for patients with neurodegenerative disorders, such as Alzheimer’s disease. Currently, two groups of biomarkers analyzed in the cerebrospinal fluid are considered – namely amyloid-β peptides and Tau proteins – along with the hyperphosphorylated forms of the latter (pTau). Current directions in the development of NDD include the following: search for novel biomarkers with improved analytical or diagnostic performance; optimization of the analysis of the biomarkers already available (e.g., by improved quality control and interlaboratory comparison of results); applications of novel technologies enabling better management of patient samples; and search for biomarkers in the blood. This article presents the state-of-the-art in the field of cerebrospinal fluid-based NDD, and also summarizes some of the hypotheses of how the future development of NDD tools might look.
TL;DR: Over 40 years of age persons with Down syndrome develop a form of dementia with several clinical and neuropathologic characteristics of Alzheimer’s disease (AD), although with an earlier age of onset.
Abstract: Down syndrome (DS) is a chromosomal abnormality due to partial or complete triplication of chromosome 21 (HSA21), and is the most common genetic cause of intellectual disability. DS may be considered a multifactorial disease, where an abnormal expression of trisomic genes arises not only from genetic, but also environ mental factors [1]. Thus, trisomy leads to a deregulated scenario that also affects disomic genes and that ultimately results in largely different phenotypes [2]. In fact, DS patients present a high variability of symptoms, including premature aging, mental retardation and Alzheimer’s-like dementia. Thus, above 40 years of age these persons develop a form of dementia with several clinical and neuropathologic characteristics of Alzheimer’s disease (AD), although with an earlier age of onset [3].
TL;DR: The application of proteomics to I/R injury and IPC to discover target proteins is reviewed and the functional meaning of the accumulated data on hundreds of proteins is analyzed using various bioinformatics applications.
Abstract: Cardiac ischemia and ischemia-reperfusion (I/R) injury are major contributors to morbidity and mortality worldwide. Pathological mechanisms of I/R and the physiological mechanisms of ischemic preconditioning (IPC), which is an effective cardiac protective response, have been widely investigated in the last decade to search for means to prevent or treat this disease. Proteomics is a powerful analytical tool that has provided important information to identify target proteins and understand the underlying mechanisms of I/R and IPC. Here, we review the application of proteomics to I/R injury and IPC to discover target proteins. We analyze the functional meaning of the accumulated data on hundreds of proteins using various bioinformatics applications. In addition, we review exercise-induced proteomic alterations in the heart to understand the potential cardioprotective role of exercise against I/R injury. Further developments in the proteomic field that target specialized proteins will yield new insights for optimizing therapeutic targets and developing a wide range of therapeutic agents against ischemic heart disease.
TL;DR: The proteomic approaches that have been used to characterize ESCs with regard to self-renewal and differentiation, with an emphasis on signaling cascades and histone modifications are described, to discuss how quantitative proteomics can be deployed to study reprogramming and iPSC identity.
Abstract: Embryonic stem cells (ESCs) are at the center stage of intense research, inspired by their potential to give rise to all cell types of the adult individual. This property makes ESCs suitable candidates for generating specialized cells to replace damaged tissue lost after injury or disease. However, such clinical applications require a detailed insight of the molecular mechanisms underlying the self-renewal, expansion and differentiation of stem cells. This has gained further relevance since the introduction of induced pluripotent stem cells (iPSCs), which are functionally very similar to ESCs. The key property that iPSCs can be derived from somatic cells lifts some of the major ethical issues related to the need for embryos to generate ESCs. Yet, this has only increased the need to define the similarity of iPSCs and ESCs at the molecular level, both before and after they are induced to differentiate. In this article, we describe the proteomic approaches that have been used to characterize ESCs with regard...
TL;DR: This article provides an overview of a variety of electrospray-based ionization methods, including nanospray, liquid chromatography and capillary electrophoresis-coupled sources, and how they are optimized for proteomic samples and discusses analyte characteristics, solvent/eluent conditions as well as optimization of ESI for top-down, bottom-up and quantitative experiments.
Abstract: Electrospray ionization (ESI) mass spectrometry is a powerful and versatile tool for proteomic analysis. By understanding how proteins and peptides behave during ESI, it is possible to predict source conditions that will maximize ionization efficiency, ultimately leading to lower detection limits for protein identification and more accurate quantitation. In this article, we provide an overview of a variety of electrospray-based ionization methods, including nanospray, liquid chromatography and capillary electrophoresis-coupled sources, and how they are optimized for proteomic samples. We will touch upon analyte characteristics, solvent/eluent conditions as well as optimization of ESI for top-down, bottom-up and quantitative experiments.
TL;DR: The purpose of this article is to focus on the recent development of proteomics and its usefulness in analyzing the human gut ecosystem and probiotic strains.
Abstract: The various bacterial communities associated with humans have many functions and the gut microbiota has a major role in the host Bacterial imbalance in the gut, known as dysbiosis, has therefore been linked to several diseases Probiotics, that is, microbial strains that have beneficial effects on the host, are thought to benefit this intestinal ecosystem Hence, knowledge of the gut microbiota composition and an understanding of its functionalities are of interest Recently, efforts have focused on developing new high-throughput techniques for studying microbial cells and complex communities Among them, proteomics is increasingly being used The purpose of this article is to focus on the recent development of this technology and its usefulness in analyzing the human gut ecosystem and probiotic strains
TL;DR: The aim of this article is to provide an overview of the various protocols available for protein biomarker discovery/validation in neurodevelopmental disorders, discuss reports in which these techniques have been previously applied, and consider the future development of this area of research.
Abstract: Protein biomarker discovery from biological fluids, such as serum, has been widely applied to disorders such as cancer and has more recently also been utilized in neuro-psychiatric disorders with relatively clear biological causes, such as Alzheimer's disease and schizophrenia. The application of the associated technologies for the identification of protein biomarker signatures in neurodevelopmental disorders, such as autism spectrum disorder and attention deficit hyperactivity disorder, is comparatively less well established. The aim of this article is to provide an overview of the various protocols available for such analysis, discuss reports in which these techniques have been previously applied in biomarker discovery/validation in neurodevelopmental disorders, and consider the future development of this area of research.
TL;DR: The recent advances in experimental strategies for measuring protein synthesis and degradation on a proteome-wide scale are outlined and the application of mass spectrometry and non-mass spectrometric-based approaches in this field of research has been discussed.
Abstract: Proteomics is a rapidly developing discipline that seeks to understand the role of proteins in the wider biological context. In order to take a holistic view of a biological system, it is vital that we can elucidate the dynamics of the proteome. In this article, we have outlined the recent advances in experimental strategies for measuring protein synthesis and degradation on a proteome-wide scale. The application of mass spectrometry and non-mass spectrometric-based approaches in this field of research has been discussed. The article also explores the challenges associated with these types of analyses and the development of appropriate bioinformatic resources for interrogating the complex datasets that are generated.
TL;DR: Recent advances in methodologies and philosophies behind several microarray-based, intermediate-level, ‘protein-omic’ methods, including a focus on reverse-phase lysate arrays and micro-western arrays, are reviewed, which have been helpful for bridging gaps between large- and small-scale protein analysis approaches and have provided insight into the roles that protein systems play in several biological processes.
Abstract: While proteomic methods have illuminated many areas of biological protein space, many fundamental questions remain with regard to systems-level relationships between mRNAs, proteins, and cell behaviors. While mass spectrometric methods offer a panoramic picture of the relative expression and modification of large numbers of proteins, they are neither optimal for the analysis of pre-defined targets across large numbers of samples nor for assessing differences in proteins between individual cells or cell compartments. Conversely, traditional antibody-based methods are effective at sensitively analyzing small numbers of proteins across small numbers of conditions, and can be used to analyze relative differences in protein abundance and modification between cells and cell compartments. However, traditional antibody-based approaches are not optimal for analyzing large numbers of protein abundances and modifications across many samples. In this perspective article, we will review recent advances in methodologies and philosophies behind several microarray-based, intermediate-level, “protein-omic” methods including a focus on reverse phase lysate arrays and micro-western arrays that have been helpful for bridging gaps between large- and small-scale protein analysis approaches and have provided insight into the roles that protein systems play in several biological processes.
TL;DR: The current challenge is developing a closer relationship between transfusion medicine and proteomics, by focusing first on the proteome identification of blood products and then on the applications and future developments within the field of proteomics and blood products.
Abstract: Proteomics has changed the way proteins are analyzed in living systems. This approach has been applied to blood products and protein profiling has evolved in parallel with the development of techniques. The identification of proteins belonging to red blood cell, platelets or plasma was achieved at the end of the last century. Then, the questions on the applications emerged. Hence, several studies have focused on problems related to blood banking and products, such as the aging of blood products, identification of biomarkers, related diseases and the protein–protein interactions. More recently, a mass spectrometry-based proteomics approach to quality control has been applied in order to offer solutions and improve the quality of blood products. The current challenge we face is developing a closer relationship between transfusion medicine and proteomics. In this article, these issues will be approached by focusing first on the proteome identification of blood products and then on the applications and future...