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1
Sadeesh, Nithin, Mauro Scaravilli, and Leena Latonen. "Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes." Cancers 13, no. 19 (September 27, 2021): 4829. http://dx.doi.org/10.3390/cancers13194829.
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Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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Masood, Afshan, Hicham Benabdelkamel, and Assim Alfadda. "Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity." High-Throughput 7, no. 3 (September 12, 2018): 27. http://dx.doi.org/10.3390/ht7030027.
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Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.
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Stubbs, Keith A., and David J. Vocadlo. "Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes." Australian Journal of Chemistry 62, no. 6 (2009): 521. http://dx.doi.org/10.1071/ch09140.
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As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.
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Solovyeva, Elizaveta M., Julia A. Bubis, Irina A. Tarasova, Anna A. Lobas, Mark V. Ivanov, Alexey A. Nazarov, Ilya A. Shutkov, and Mikhail V. Gorshkov. "On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics." Biochemistry (Moscow) 87, no. 11 (November 2022): 1342–53. http://dx.doi.org/10.1134/s000629792211013x.
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Abstract Protein quantitation in tissue cells or physiological fluids based on liquid chromatography/mass spectrometry is one of the key sources of information on the mechanisms of cell functioning during chemotherapeutic treatment. Information on significant changes in protein expression upon treatment can be obtained by chemical proteomics and requires analysis of the cellular proteomes, as well as development of experimental and bioinformatic methods for identification of the drug targets. Low throughput of whole proteome analysis based on liquid chromatography and tandem mass spectrometry is one of the main factors limiting the scale of these studies. The method of direct mass spectrometric identification of proteins, DirectMS1, is one of the approaches developed in recent years allowing ultrafast proteome-wide analyses employing minute-scale gradients for separation of proteolytic mixtures. Aim of this work was evaluation of both possibilities and limitations of the method for identification of drug targets at the level of whole proteome and for revealing cellular processes activated by the treatment. Particularly, the available literature data on chemical proteomics obtained earlier for a large set of onco-pharmaceuticals using multiplex quantitative proteome profiling were analyzed. The results obtained were further compared with the proteome-wide data acquired by the DirectMS1 method using ultrashort separation gradients to evaluate efficiency of the method in identifying known drug targets. Using ovarian cancer cell line A2780 as an example, a whole-proteome comparison of two cell lysis techniques was performed, including the freeze-thaw lysis commonly employed in chemical proteomics and the one based on ultrasonication for cell disruption, which is the widely accepted as a standard in proteomic studies. Also, the proteome-wide profiling was performed using ultrafast DirectMS1 method for A2780 cell line treated with lonidamine, followed by gene ontology analyses to evaluate capabilities of the method in revealing regulation of proteins in the cellular processes associated with drug treatment.
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Agarwal, Ashok, Manesh Kumar Panner Selvam, and Saradha Baskaran. "Proteomic Analyses of Human Sperm Cells: Understanding the Role of Proteins and Molecular Pathways Affecting Male Reproductive Health." International Journal of Molecular Sciences 21, no. 5 (February 27, 2020): 1621. http://dx.doi.org/10.3390/ijms21051621.
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Human sperm proteomics research has gained increasing attention lately, which provides complete information about the functional state of the spermatozoa. Changes in the sperm proteome are evident in several male infertility associated conditions. Global proteomic tools, such as liquid chromatography tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight, are used to profile the sperm proteins to identify the molecular pathways that are defective in infertile men. This review discusses the use of proteomic techniques to analyze the spermatozoa proteome. It also highlights the general steps involved in global proteomic approaches including bioinformatic analysis of the sperm proteomic data. Also, we have presented the findings of major proteomic studies and possible biomarkers in the diagnosis and therapeutics of male infertility. Extensive research on sperm proteome will help in understanding the role of fertility associated sperm proteins. Validation of the sperm proteins as biomarkers in different male infertility conditions may aid the physician in better clinical management.
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Burat, Bastien, Audrey Reynaerts, Dominique Baiwir, Maximilien Fléron, Gauthier Eppe, Teresinha Leal, and Gabriel Mazzucchelli. "Characterization of the Human Eccrine Sweat Proteome—A Focus on the Biological Variability of Individual Sweat Protein Profiles." International Journal of Molecular Sciences 22, no. 19 (October 8, 2021): 10871. http://dx.doi.org/10.3390/ijms221910871.
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The potential of eccrine sweat as a bio-fluid of interest for diagnosis and personalized therapy has not yet been fully evaluated, due to the lack of in-depth sweat characterization studies. Thanks to recent developments in omics, together with the availability of accredited sweat collection methods, the analysis of human sweat may now be envisioned as a standardized, non-invasive test for individualized monitoring and personalized medicine. Here, we characterized individual sweat samples, collected from 28 healthy adult volunteers under the most standardized sampling methodology, by applying optimized shotgun proteomics. The thorough characterization of the sweat proteome allowed the identification of 983 unique proteins from which 344 were identified across all samples. Annotation-wise, the study of the sweat proteome unveiled the over-representation of newly addressed actin dynamics, oxidative stress and proteasome-related functions, in addition to well-described proteolysis and anti-microbial immunity. The sweat proteome composition correlated with the inter-individual variability of sweat secretion parameters. In addition, both gender-exclusive proteins and gender-specific protein abundances were highlighted, despite the high similarity between human female and male sweat proteomes. In conclusion, standardized sample collection coupled with optimized shotgun proteomics significantly improved the depth of sweat proteome coverage, far beyond previous similar studies. The identified proteins were involved in many diverse biological processes and molecular functions, indicating the potential of this bio-fluid as a valuable biological matrix for further studies. Addressing sweat variability, our results prove the proteomic profiling of sweat to be a promising bio-fluid analysis for individualized, non-invasive monitoring and personalized medicine.
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Han, Mee-Jung, and Sang Yup Lee. "The Escherichia coli Proteome: Past, Present, and Future Prospects." Microbiology and Molecular Biology Reviews 70, no. 2 (June 2006): 362–439. http://dx.doi.org/10.1128/mmbr.00036-05.
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SUMMARY Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.
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Sobolev, Vladimir V., Anna G. Soboleva, Elena V. Denisova, Eva A. Pechatnikova, Eugenia Dvoryankova, Irina M. Korsunskaya, and Alexandre Mezentsev. "Proteomic Studies of Psoriasis." Biomedicines 10, no. 3 (March 7, 2022): 619. http://dx.doi.org/10.3390/biomedicines10030619.
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In this review paper, we discuss the contribution of proteomic studies to the discovery of disease-specific biomarkers to monitor the disease and evaluate available treatment options for psoriasis. Psoriasis is one of the most prevalent skin disorders driven by a Th17-specific immune response. Although potential patients have a genetic predisposition to psoriasis, the etiology of the disease remains unknown. During the last two decades, proteomics became deeply integrated with psoriatic research. The data obtained in proteomic studies facilitated the discovery of novel mechanisms and the verification of many experimental hypotheses of the disease pathogenesis. The detailed data analysis revealed multiple differentially expressed proteins and significant changes in proteome associated with the disease and drug efficacy. In this respect, there is a need for proteomic studies to characterize the role of the disease-specific biomarkers in the pathogenesis of psoriasis, develop clinical applications to choose the most efficient treatment options and monitor the therapeutic response.
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Campanati, Anna, Emanuela Martina, Federico Diotallevi, Giulia Radi, Andrea Marani, Davide Sartini, Monica Emanuelli, et al. "Saliva Proteomics as Fluid Signature of Inflammatory and Immune-Mediated Skin Diseases." International Journal of Molecular Sciences 22, no. 13 (June 29, 2021): 7018. http://dx.doi.org/10.3390/ijms22137018.
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Saliva is easy to access, non-invasive and a useful source of information useful for the diagnosis of serval inflammatory and immune-mediated diseases. Following the advent of genomic technologies and -omic research, studies based on saliva testing have rapidly increased and human salivary proteome has been partially characterized. As a proteomic protocol to analyze the whole saliva proteome is not currently available, the most common aim of the proteomic analysis is to discriminate between physiological and pathological conditions. The salivary proteome has been initially investigated in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease, and Sjögren’s syndrome. Otherwise, salivary proteomics studies in the dermatological field are still in the initial phase, thus the aim of this review is to collect the best research evidence on the role of saliva proteomics analysis in immune-mediated skin diseases to understand the direction of research in this field. The results of PRISMA analysis reported herein suggest that human saliva analysis could provide significant data for the diagnosis and prognosis of several immune-mediated and inflammatory skin diseases in the next future.
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Bespyatykh, Ju A., E. A. Shitikov, and E. N. Ilina. "Proteomics for the Investigation of Mycobacteria." Acta Naturae 9, no. 1 (March 15, 2017): 15–25. http://dx.doi.org/10.32607/20758251-2017-9-1-15-25.
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The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
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Pitteri, Sharon, and Sam Hanash. "A Systems Approach to the Proteomic Identification of Novel Cancer Biomarkers." Disease Markers 28, no. 4 (2010): 233–39. http://dx.doi.org/10.1155/2010/270859.
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The proteomics field has experienced rapid growth with technologies achieving ever increasing accuracy, sensitivity, and throughput, and with availability of computational tools to address particular applications. Given that the proteome represents the most functional component encoded for in the genome, a systems approach to disease investigations and biomarker identification benefits substantially from integration of proteome level studies. Here we present proteomic approaches that have allowed systematic searches for potential cancer markers by integrating cancer cell profiling with additional sources of data, as illustrated with recent studies of ovarian cancer.
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Poetsch, Ansgar, and María Inés Marchesini. "Proteomics of Brucella." Proteomes 8, no. 2 (April 22, 2020): 8. http://dx.doi.org/10.3390/proteomes8020008.
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Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the molecular mechanisms underlying Brucella pathogenesis. Technological and methodological advancements such as increased instrument performance and multiplexed quantification have broadened the range of proteome studies, enabling new and improved analyses, providing deeper and more accurate proteome coverage. Indeed, proteomics has demonstrated its contribution to key research questions in Brucella biology, i.e., immunodominant proteins, host-cell interaction, stress response, antibiotic targets and resistance, protein secretion. Here, we review the proteomics of Brucella with a focus on more recent works and novel findings, ranging from reconfiguration of the intracellular bacterial proteome and studies on proteomic profiles of Brucella infected tissues, to the identification of Brucella extracellular proteins with putative roles in cell signaling and pathogenesis. In conclusion, proteomics has yielded copious new candidates and hypotheses that require future verification. It is expected that proteomics will continue to be an invaluable tool for Brucella and applications will further extend to the currently ill-explored aspects including, among others, protein processing and post-translational modification.
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Balotf, Sadegh, Richard Wilson, Robert S. Tegg, David S. Nichols, and Calum R. Wilson. "Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions." Proteomes 10, no. 1 (January 19, 2022): 5. http://dx.doi.org/10.3390/proteomes10010005.
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The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant–pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant–pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant–pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant–pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Chalmel, Frédéric, and Antoine D. Rolland. "Linking transcriptomics and proteomics in spermatogenesis." REPRODUCTION 150, no. 5 (November 2015): R149—R157. http://dx.doi.org/10.1530/rep-15-0073.
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Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the ‘proteomics informed by transcriptomics’ technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.
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Hohn, Andreas, Ivan Iovino, Fabrizio Cirillo, Hendrik Drinhaus, Kathrin Kleinbrahm, Lennert Boehm, Edoardo De Robertis, and Jochen Hinkelbein. "Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney) and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers." BioMed Research International 2018 (March 21, 2018): 1–11. http://dx.doi.org/10.1155/2018/3576157.
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During the last years, proteomic studies have revealed several interesting findings in experimental sepsis models and septic patients. However, most studies investigated protein alterations only in single organs or in whole blood. To identify possible sepsis biomarkers and to evaluate the relationship between protein alteration in sepsis affected organs and blood, proteomics data from the heart, brain, liver, kidney, and serum were analysed. Using functional network analyses in combination with hierarchical cluster analysis, we found that protein regulation patterns in organ tissues as well as in serum are highly dynamic. In the tissue proteome, the main functions and pathways affected were the oxidoreductive activity, cell energy generation, or metabolism, whereas in the serum proteome, functions were associated with lipoproteins metabolism and, to a minor extent, with coagulation, inflammatory response, and organ regeneration. Proteins from network analyses of organ tissue did not correlate with statistically significantly regulated serum proteins or with predicted proteins of serum functions. In this study, the combination of proteomic network analyses with cluster analyses is introduced as an approach to deal with high-throughput proteomics data to evaluate the dynamics of protein regulation during sepsis.
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Kwon, Dami, Jong-Moon Park, Van-An Duong, Seong-Joo Hong, Byung-Kwan Cho, Choul-Gyun Lee, Hyung-Kyoon Choi, Dong-Myung Kim, and Hookeun Lee. "Comparative Proteomic Profiling of Marine and Freshwater Synechocystis Strains Using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Marine Science and Engineering 8, no. 10 (October 12, 2020): 790. http://dx.doi.org/10.3390/jmse8100790.
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Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.
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Kruse, Rikke, Navid Sahebekhtiari, and Kurt Højlund. "The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance." International Journal of Molecular Sciences 21, no. 15 (July 28, 2020): 5374. http://dx.doi.org/10.3390/ijms21155374.
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Introduction: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the currently available studies characterizing the mitochondrial proteome in human skeletal muscle in insulin-resistant conditions, such as obesity, T2D, and aging, as well as exercise-mediated changes in the mitochondrial proteome. Furthermore, we outline technical challenges and limitations and methodological aspects that should be considered when planning future large-scale proteomics studies of mitochondria from human skeletal muscle. Authors’ view: At present, most proteomic studies of skeletal muscle or isolated muscle mitochondria have demonstrated a reduced abundance of proteins in several mitochondrial biological processes in obesity, T2D, and aging, whereas the beneficial effects of exercise involve an increased content of muscle proteins involved in mitochondrial metabolism. Powerful mass-spectrometry-based proteomics now provides unprecedented opportunities to perform in-depth proteomics of muscle mitochondria, which in the near future is expected to increase our understanding of the complex molecular mechanisms underlying the link between mitochondrial dysfunction and insulin resistance in chronic metabolic disorders.
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Nguyen, Nam H. K., Huiyun Wu, Haiyan Tan, Junmin Peng, Jeffrey E. Rubnitz, Xueyuan Cao, Stanley Pounds, and Jatinder K. Lamba. "Global Proteomic Profiling of Pediatric AML: A Pilot Study." Cancers 13, no. 13 (June 24, 2021): 3161. http://dx.doi.org/10.3390/cancers13133161.
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Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML’s heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limited. Furthermore, the majority of biological functions within cells are operated by proteins (i.e., enzymes) and most drugs target the proteome rather than the genome or transcriptome, thus, highlighting the significance of studying proteomics. Here, we present our results from a pilot study investigating global proteomic profiles of leukemic cells obtained at diagnosis from 16 pediatric AML patients using a robust TMT-LC/LC-MS/MS platform. The proteome profiles were compared among patients with or without core binding factor (CBF) translocation indicated by a t(8;21) or inv(16) cytogenetic abnormality, minimal residual disease status at the end of the first cycle of chemotherapy (MRD1), and in vitro chemosensitivity of leukemic cells to cytarabine (Ara-C LC50). Our results established proteomic differences between CBF and non-CBF AML subtypes, providing insights to AML subtypes physiology, and identified potential druggable proteome targets such as THY1 (CD90), NEBL, CTSF, COL2A1, CAT, MGLL (MAGL), MACROH2A2, CLIP2 (isoform 1 and 2), ANPEP (CD13), MMP14, and AK5.
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Semančíková, E., S. Tkáčiková, I. Talian, M. Bencková, E. Pálová, and J. Sabo. "In Search of Possible Peripheral Biomarkers for Suicide: Similarities Between Platelet and Cerebrospinal Fluid Proteome (Preliminary Results)." European Psychiatry 41, S1 (April 2017): S638. http://dx.doi.org/10.1016/j.eurpsy.2017.01.1051.
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Despite the fact that proteomic analysis is becoming widely used in various medical branches its use in psychiatry is still very limited. Majority of psychiatric proteomic research is still oriented mostly on Alzheimer's disease, schizophrenia and depression but very few studies focus on suicidality. We decided, based on the current knowledge, to study suicidal behaviour with the use of proteomics to compare cerebrospinal fluid and platelets. We hypothesized that the same protein group can be detected in pathways that are part of platelet degranulation process in the platelet proteome and cerebrospinal fluid proteome. Based on these findings we suppose, that with use of proteomic analysis a specific protein (group of proteins) can be identified in both, cerebrospinal fluid and platelet proteome in patients with suicidal behavior.Group of proteins identified in our sample in the reactome pathway database (release of platelet secretary granule components and exocytosis of platelet granule contents) supports the idea of link between central nervous system and platelets (“the periphery”). Further research is needed to clarify whether the identified group of proteins taking part in platelet pathways can be used as peripheral biomarkers for suicidal behavior.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Bonomini, Mario, Luisa Pieroni, Maurizio Ronci, Vittorio Sirolli, and Andrea Urbani. "Blood Cell Proteomics in Chronic Kidney Disease." Open Urology & Nephrology Journal 11, no. 1 (July 31, 2018): 28–38. http://dx.doi.org/10.2174/1874303x01811010028.
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Background: The uremic syndrome mimes a systemic poisoning with the retention of numerous compounds which are normally removed by the kidney. The study of proteins and peptides, or proteomics, represents an important field of research for the investigation of blood and blood diseases. Methods and Materials: We focused our review on the results of proteomic investigations on blood cells of uremic patients with particular regard to the study of red blood cells, platelets, and monocytes. Results: In literature there are few, preliminary studies on platelets and monocytes while the knowledge on uremic erythrocytes is much wider. Proteomic investigations showed that erythrocyte membrane proteome of uremic patients, differs significantly from the proteome of healthy subjects, being characterized by an extensive remodeling which may influence visco-elastic properties of RBC such as deformability and involve diverse molecular pathways driving red blood cell signaling and removal. Conclusion: Proteomic technologies emerged as a useful tool in defining and characterizing both physiological and disease processes being able, among others, to give important insights into uremic anemia.
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Mahajan, R., and P. Gupta. "Proteomics: taking over where genomics leaves off." Czech Journal of Genetics and Plant Breeding 46, No. 2 (June 29, 2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.
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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides the qualitative and quantitative description of the expressed proteins, proteomics also deals with the analysis of mutual interactions of proteins. Thereby, candidate proteins can be identified which may be used as starting-points for diagnostic or even therapeutic approaches.
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Moghieb, Ahmed, Geremy Clair, Hugh D. Mitchell, Joseph Kitzmiller, Erika M. Zink, Young-Mo Kim, Vladislav Petyuk, et al. "Time-resolved proteome profiling of normal lung development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1 (July 1, 2018): L11—L24. http://dx.doi.org/10.1152/ajplung.00316.2017.
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Biochemical networks mediating normal lung morphogenesis and function have important implications for ameliorating morbidity and mortality in premature infants. Although several transcript-level studies have examined normal lung development, corresponding protein-level analyses are lacking. Here we performed proteomics analysis of murine lungs from embryonic to early adult ages to identify the molecular networks mediating normal lung development. We identified 8,932 proteins, providing a deep and comprehensive view of the lung proteome. Analysis of the proteomics data revealed discrete modules and the underlying regulatory and signaling network modulating their expression during development. Our data support the cell proliferation that characterizes early lung development and highlight responses of the lung to exposure to a nonsterile oxygen-rich ambient environment and the important role of lipid (surfactant) metabolism in lung development. Comparison of dynamic regulation of proteomic and recent transcriptomic analyses identified biological processes under posttranscriptional control. Our study provides a unique proteomic resource for understanding normal lung formation and function and can be freely accessed at Lungmap.net.
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Eligini, Sonia, Erica Gianazza, Alice Mallia, Stefania Ghilardi, and Cristina Banfi. "Macrophage Phenotyping in Atherosclerosis by Proteomics." International Journal of Molecular Sciences 24, no. 3 (January 30, 2023): 2613. http://dx.doi.org/10.3390/ijms24032613.
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Macrophages are heterogeneous and plastic cells, able to adapt their phenotype and functions to changes in the microenvironment. They are involved in several homeostatic processes and also in many human diseases, including atherosclerosis, where they participate in all the stages of the disease. For these reasons, macrophages have been studied extensively using different approaches, including proteomics. Proteomics, indeed, may be a powerful tool to better understand the behavior of these cells, and a careful analysis of the proteome of different macrophage phenotypes can help to better characterize the role of these phenotypes in atherosclerosis and provide a broad view of proteins that might potentially affect the course of the disease. In this review, we discuss the different proteomic techniques that have been used to delineate the proteomic profile of macrophage phenotypes and summarize some results that can help to elucidate the roles of macrophages and develop new strategies to counteract the progression of atherosclerosis and/or promote regression.
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Meng, Zhaoyang, Ran You, Arif Mahmood, Fancheng Yan, and Yanling Wang. "Application of Proteomics Analysis and Animal Models in Optic Nerve Injury Diseases." Brain Sciences 13, no. 3 (February 26, 2023): 404. http://dx.doi.org/10.3390/brainsci13030404.
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Optic nerve damage is a common cause of blindness. Optic nerve injury is often accompanied by fundus vascular disease, retinal ganglion cell apoptosis, and changes in retinal thickness. These changes can cause alterations in protein expression within neurons in the retina. Proteomics analysis offers conclusive evidence to decode a biological system. Furthermore, animal models of optic nerve injury made it possible to gain insight into pathological mechanisms, therapeutic targets, and effective treatment of such injuries. Proteomics takes the proteome as the research object and studies protein changes in cells and tissues. At present, a variety of proteomic analysis methods have been widely used in the research of optic nerve injury diseases. This review summarizes the application of proteomic research in optic nerve injury diseases and animal models of optic nerve injury. Additionally, differentially expressed proteins are summarized and analyzed. Various optic nerve injuries, including those associated with different etiologies, are discussed along with their potential therapeutic targets and future directions.
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Angi, Martina, Helen Kalirai, Sarah E. Coupland, Bertil E. Damato, Francesco Semeraro, and Mario R. Romano. "Proteomic Analyses of the Vitreous Humour." Mediators of Inflammation 2012 (2012): 1–7. http://dx.doi.org/10.1155/2012/148039.
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The human vitreous humour (VH) is a transparent, highly hydrated gel, which occupies the posterior segment of the eye between the lens and the retina. Physiological and pathological conditions of the retina are reflected in the protein composition of the VH, which can be sampled as part of routine surgical procedures. Historically, many studies have investigated levels of individual proteins in VH from healthy and diseased eyes. In the last decade, proteomics analyses have been performed to characterise the proteome of the human VH and explore networks of functionally related proteins, providing insight into the aetiology of diabetic retinopathy and proliferative vitreoretinopathy. Recent proteomic studies on the VH from animal models of autoimmune uveitis have identified new signalling pathways associated to autoimmune triggers and intravitreal inflammation. This paper aims to guide biological scientists through the different proteomic techniques that have been used to analyse the VH and present future perspectives for the study of intravitreal inflammation using proteomic analyses.
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Petriz, Bernardo A., and Octavio L. Franco. "Effects of Hypertension and Exercise on Cardiac Proteome Remodelling." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/634132.
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Left ventricle hypertrophy is a common outcome of pressure overload stimulus closely associated with hypertension. This process is triggered by adverse molecular signalling, gene expression, and proteome alteration. Proteomic research has revealed that several molecular targets are associated with pathologic cardiac hypertrophy, including angiotensin II, endothelin-1 and isoproterenol. Several metabolic, contractile, and stress-related proteins are shown to be altered in cardiac hypertrophy derived by hypertension. On the other hand, exercise is a nonpharmacologic agent used for hypertension treatment, where cardiac hypertrophy induced by exercise training is characterized by improvement in cardiac function and resistance against ischemic insult. Despite the scarcity of proteomic research performed with exercise, healthy and pathologic heart proteomes are shown to be modulated in a completely different way. Hence, the altered proteome induced by exercise is mostly associated with cardioprotective aspects such as contractile and metabolic improvement and physiologic cardiac hypertrophy. The present review, therefore, describes relevant studies involving the molecular characteristics and alterations from hypertensive-induced and exercise-induced hypertrophy, as well as the main proteomic research performed in this field. Furthermore, proteomic research into the effect of hypertension on other target-demerged organs is examined.
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Gajahin Gamage, Nadeeka Thushari, Rina Miyashita, Kazutaka Takahashi, Shuichi Asakawa, and Jayan Duminda Mahesh Senevirathna. "Proteomic Applications in Aquatic Environment Studies." Proteomes 10, no. 3 (September 1, 2022): 32. http://dx.doi.org/10.3390/proteomes10030032.
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Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Hill, Jennifer J., Arsalan S. Haqqani, and Danica B. Stanimirovic. "Proteome of the Luminal Surface of the Blood–Brain Barrier." Proteomes 9, no. 4 (November 10, 2021): 45. http://dx.doi.org/10.3390/proteomes9040045.
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Interrogation of the molecular makeup of the blood–brain barrier (BBB) using proteomic techniques has contributed to the cataloguing and functional understanding of the proteins uniquely organized at this specialized interface. The majority of proteomic studies have focused on cellular components of the BBB, including cultured brain endothelial cells (BEC). Detailed proteome mapping of polarized BEC membranes and their intracellular endosomal compartments has led to an improved understanding of the processes leading to internalization and transport of various classes of molecules across the BBB. Quantitative proteomic methods have further enabled absolute and comparative quantification of key BBB transporters and receptors in isolated BEC and microvessels from various species. However, translational studies further require in vivo/in situ analyses of the proteins exposed on the luminal surface of BEC in vessels under various disease and treatment conditions. In vivo proteomics approaches, both profiling and quantitative, usually rely on ‘capturing’ luminally-exposed proteins after perfusion with chemical labeling reagents, followed by analysis with various mass spectrometry-based approaches. This manuscript reviews recent advances in proteomic analyses of luminal membranes of BEC in vitro and in vivo and their applications in translational studies focused on developing novel delivery methods across the BBB.
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Björkeroth, Johan, Kate Campbell, Carl Malina, Rosemary Yu, Francesca Di Bartolomeo, and Jens Nielsen. "Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media." Proceedings of the National Academy of Sciences 117, no. 35 (August 17, 2020): 21804–12. http://dx.doi.org/10.1073/pnas.1921890117.
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Several recent studies have shown that the concept of proteome constraint, i.e., the need for the cell to balance allocation of its proteome between different cellular processes, is essential for ensuring proper cell function. However, there have been no attempts to elucidate how cells’ maximum capacity to grow depends on protein availability for different cellular processes. To experimentally address this, we cultivatedSaccharomyces cerevisiaein bioreactors with or without amino acid supplementation and performed quantitative proteomics to analyze global changes in proteome allocation, during both anaerobic and aerobic growth on glucose. Analysis of the proteomic data implies that proteome mass is mainly reallocated from amino acid biosynthetic processes into translation, which enables an increased growth rate during supplementation. Similar findings were obtained from both aerobic and anaerobic cultivations. Our findings show that cells can increase their growth rate through increasing its proteome allocation toward the protein translational machinery.
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Panner Selvam, Manesh, Ashok Agarwal, Tânia Dias, Ana Martins, and Luna Samanta. "Presence of Round Cells Proteins do not Interfere with Identification of Human Sperm Proteins from Frozen Semen Samples by LC-MS/MS." International Journal of Molecular Sciences 20, no. 2 (January 14, 2019): 314. http://dx.doi.org/10.3390/ijms20020314.
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In sperm proteomic experiments round cells and leukocyte proteins are profiled along with sperm proteome. The influence of round cell and leukocyte proteins on the sperm proteome has not been investigated. The objective of this study was to identify if the proteins from round cells, including leukocytes, interfere with the proteomic analysis of spermatozoa in frozen semen samples. Proteomic profiling of sperm was performed using liquid chromatography-tandem mass spectrometry in four groups: Group 1 contained neat semen with round cells and leukocytes ≥ 1 × 106/mL, group 2 contained neat semen with round cells ≥ 1 × 106/mL that was processed by 65% density gradient to remove the round cells and leukocytes, group 3 contained neat semen with round cells < 1 × 106/mL, and group 4 contained neat semen with round cells < 1 × 106/mL that was processed by 65% density gradient to remove the round cells. Pure leukocyte culture was used as control group. A total of 1638, 1393, 1755, and 1404 proteins were identified in groups 1, 2, 3, and 4, respectively. Comparative analysis of group 1 vs. 3 revealed 26 (1.18%) differentially expressed proteins (DEPs). On the other hand, only 6 (0.31%) DEPs were observed with group 2 vs. 4. Expression of these DEPs were either absent or very low in the control group. The results of our proteomics analysis failed to show any influence of non-spermatogenic round cell proteins on sperm proteome identification. These results validate the use of neat semen samples for sperm proteomic studies.
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Gianazza, Erica, Maura Brioschi, Roberta Baetta, Alice Mallia, Cristina Banfi, and Elena Tremoli. "Platelets in Healthy and Disease States: From Biomarkers Discovery to Drug Targets Identification by Proteomics." International Journal of Molecular Sciences 21, no. 12 (June 25, 2020): 4541. http://dx.doi.org/10.3390/ijms21124541.
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Platelets are a heterogeneous small anucleate blood cell population with a central role both in physiological haemostasis and in pathological states, spanning from thrombosis to inflammation, and cancer. Recent advances in proteomic studies provided additional important information concerning the platelet biology and the response of platelets to several pathophysiological pathways. Platelets circulate systemically and can be easily isolated from human samples, making proteomic application very interesting for characterizing the complexity of platelet functions in health and disease as well as for identifying and quantifying potential platelet proteins as biomarkers and novel antiplatelet therapeutic targets. To date, the highly dynamic protein content of platelets has been studied in resting and activated platelets, and several subproteomes have been characterized including platelet-derived microparticles, platelet granules, platelet releasates, platelet membrane proteins, and specific platelet post-translational modifications. In this review, a critical overview is provided on principal platelet proteomic studies focused on platelet biology from signaling to granules content, platelet proteome changes in several diseases, and the impact of drugs on platelet functions. Moreover, recent advances in quantitative platelet proteomics are discussed, emphasizing the importance of targeted quantification methods for more precise, robust and accurate quantification of selected proteins, which might be used as biomarkers for disease diagnosis, prognosis and therapy, and their strong clinical impact in the near future.
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Dolgalev, Georgii V., Taras A. Safonov, Viktoriia A. Arzumanian, Olga I. Kiseleva, and Ekaterina V. Poverennaya. "Estimating Total Quantitative Protein Content in Escherichia coli, Saccharomyces cerevisiae, and HeLa Cells." International Journal of Molecular Sciences 24, no. 3 (January 20, 2023): 2081. http://dx.doi.org/10.3390/ijms24032081.
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The continuous improvement of proteomic techniques, most notably mass spectrometry, has generated quantified proteomes of many organisms with unprecedented depth and accuracy. However, there is still a significant discrepancy in the reported numbers of total protein molecules per specific cell type. In this article, we explore the results of proteomic studies of Escherichia coli, Saccharomyces cerevisiae, and HeLa cells in terms of total protein copy numbers per cell. We observe up to a ten-fold difference between reported values. Investigating possible reasons for this discrepancy, we conclude that neither an unmeasured fraction of the proteome nor biases in the quantification of individual proteins can explain the observed discrepancy. We normalize protein copy numbers in each study using a total protein amount per cell as reported in the literature and create integrated proteome maps of the selected model organisms. Our results indicate that cells contain from one to three million protein molecules per µm3 and that protein copy density decreases with increasing organism complexity.
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Wu, Jinlu, Qingsong Lin, Teck Kwang Lim, Tiefei Liu, and Choy-Leong Hew. "White Spot Syndrome Virus Proteins and Differentially Expressed Host Proteins Identified in Shrimp Epithelium by Shotgun Proteomics and Cleavable Isotope-Coded Affinity Tag." Journal of Virology 81, no. 21 (August 22, 2007): 11681–89. http://dx.doi.org/10.1128/jvi.01006-07.
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ABSTRACT Shrimp subcuticular epithelial cells are the initial and major targets of white spot syndrome virus (WSSV) infection. Proteomic studies of WSSV-infected subcuticular epithelium of Penaeus monodon were performed through two approaches, namely, subcellular fractionation coupled with shotgun proteomics to identify viral and host proteins and a quantitative time course proteomic analysis using cleavable isotope-coded affinity tags (cICATs) to identify differentially expressed cellular proteins. Peptides were analyzed by offline coupling of two-dimensional liquid chromatography with matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry. We identified 27, 20, and 4 WSSV proteins from cytosolic, nuclear, and membrane fractions, respectively. Twenty-eight unique WSSV proteins with high confidence (total ion confidence interval percentage [CI%], >95%) were observed, 11 of which are reported here for the first time, and 3 of these novel proteins were shown to be viral nonstructural proteins by Western blotting analysis. A first shrimp protein data set containing 1,999 peptides (ion score, ≥20) and 429 proteins (total ion score CI%, >95%) was constructed via shotgun proteomics. We also identified 10 down-regulated proteins and 2 up-regulated proteins from the shrimp epithelial lysate via cICAT analysis. This is the first comprehensive study of WSSV-infected epithelia by proteomics. The 11 novel viral proteins represent the latest addition to our knowledge of the WSSV proteome. Three proteomic data sets consisting of WSSV proteins, epithelial cellular proteins, and differentially expressed cellular proteins generated in the course of WSSV infection provide a new resource for further study of WSSV-shrimp interactions.
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Matt, Peter, Zongming Fu, Qin Fu, and Jennifer E. Van Eyk. "Biomarker discovery: proteome fractionation and separation in biological samples." Physiological Genomics 33, no. 1 (March 2008): 12–17. http://dx.doi.org/10.1152/physiolgenomics.00282.2007.
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Proteomics, analogous with genomics, is the analysis of the protein complement present in a cell, organ, or organism at any given time. While the genome provides information about the theoretical status of the cellular proteins, the proteome describes the actual content, which ultimately determines the phenotype. The broad application of proteomic technologies in basic science and clinical medicine has the potential to accelerate our understanding of the molecular mechanisms underlying disease and may facilitate the discovery of new drug targets and diagnostic disease markers. Proteomics is a rapidly developing and changing scientific discipline, and the last 5 yr have seen major advances in the underlying techniques as well as expansion into new applications. Core technologies for the separation of proteins and/or peptides are one- and two-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography, and these are coupled almost exclusively with mass spectrometry. Proteomic studies have shown that the most effective analysis of even simple biological samples requires subfractionation and/or enrichment before protein identification by mass spectrometry. Selection of the appropriate technology or combination of technologies to match the biological questions is essential for maximum coverage of the selected subproteome and to ensure both the full interpretation and the downstream utility of the data. In this review, we describe the current technologies for proteome fractionation and separation of biological samples, based on our lab workflow for biomarker discovery and validation.
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Ji, Qing, Fangshi Zhu, Xuan Liu, Qi Li, and Shi-bing Su. "Recent Advance in Applications of Proteomics Technologies on Traditional Chinese Medicine Research." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/983139.
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Proteomics technology, a major component of system biology, has gained comprehensive attention in the area of medical diagnosis, drug development, and mechanism research. On the holistic and systemic theory, proteomics has a convergence with traditional Chinese medicine (TCM). In this review, we discussed the applications of proteomic technologies in diseases-TCM syndrome combination researches. We also introduced the proteomic studies on thein vivoandin vitroeffects and underlying mechanisms of TCM treatments using Chinese herbal medicine (CHM), Chinese herbal formula (CHF), and acupuncture. Furthermore, the combined studies of proteomics with other “-omics” technologies in TCM were also discussed. In summary, this report presents an overview of the recent advances in the application of proteomic technologies in TCM studies and sheds a light on the future global and further research on TCM.
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Holland, Ashling, and Kay Ohlendieck. "Proteomic Profiling of the Dystrophin-DeficientmdxPhenocopy of Dystrophinopathy-Associated Cardiomyopathy." BioMed Research International 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/246195.
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Cardiorespiratory complications are frequent symptoms of Duchenne muscular dystrophy, a neuromuscular disorder caused by primary abnormalities in the dystrophin gene. Loss of cardiac dystrophin initially leads to changes in dystrophin-associated glycoproteins and subsequently triggers secondarily sarcolemmal disintegration, fibre necrosis, fibrosis, fatty tissue replacement, and interstitial inflammation. This results in progressive cardiac disease, which is the cause of death in a considerable number of patients afflicted with X-linked muscular dystrophy. In order to better define the molecular pathogenesis of this type of cardiomyopathy, several studies have applied mass spectrometry-based proteomics to determine proteome-wide alterations in dystrophinopathy-associated cardiomyopathy. Proteomic studies included both gel-based and label-free mass spectrometric surveys of dystrophin-deficient heart muscle from the establishedmdxanimal model of dystrophinopathy. Comparative cardiac proteomics revealed novel changes in proteins associated with mitochondrial energy metabolism, glycolysis, signaling, iron binding, antibody response, fibre contraction, basal lamina stabilisation, and cytoskeletal organisation. This review summarizes the importance of studying cardiomyopathy within the field of muscular dystrophy research, outlines key features of themdxheart and its suitability as a model system for studying cardiac pathogenesis, and discusses the impact of recent proteomic findings for exploring molecular and cellular aspects of cardiac abnormalities in inherited muscular dystrophies.
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Gnatenko, Dmitri V., Peter L. Perrotta, and Wadie F. Bahou. "Proteomic approaches to dissect platelet function: half the story." Blood 108, no. 13 (December 15, 2006): 3983–91. http://dx.doi.org/10.1182/blood-2006-06-026518.
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AbstractPlatelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platelet proteome in normal and pathologic states. The integration of transcriptomics and proteomics, coupled with progress in bioinformatics, provides novel tools for dissecting platelet biology. In this review, we focus on current advances in platelet proteomic studies, with emphasis on the importance of parallel transcriptomic studies to optimally dissect platelet function. Applications of these global profiling approaches to investigate platelet genetic diseases and platelet-related disorders are also addressed.
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Kondo, Tadashi, Daisuke Kubota, and Akira Kawai. "Application of Proteomics to Soft Tissue Sarcomas." International Journal of Proteomics 2012 (June 19, 2012): 1–15. http://dx.doi.org/10.1155/2012/876401.
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Soft tissue sarcomas are rare and account for less than 1% of all malignant cancers. Other than development of intensive therapies, the clinical outcome of patients with soft tissue sarcoma remains very poor, particularly when diagnosed at a late stage. Unique mutations have been associated with certain soft tissue sarcomas, but their etiologies remain unknown. The proteome is a functional translation of a genome, which directly regulates the malignant features of tumors. Thus, proteomics is a promising approach for investigating soft tissue sarcomas. Various proteomic approaches and clinical materials have been used to address clinical and biological issues, including biomarker development, molecular target identification, and study of disease mechanisms. Several cancer-associated proteins have been identified using conventional technologies such as 2D-PAGE, mass spectrometry, and array technology. The functional backgrounds of proteins identified were assessed extensively using in vitro experiments, thus supporting expression analysis. These observations demonstrate the applicability of proteomics to soft tissue sarcoma studies. However, the sample size in each study was insufficient to allow conclusive results. Given the low frequency of soft tissue sarcomas, multi-institutional collaborations are required to validate the results of proteomic approaches.
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Wang, Xuchu. "Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era." International Journal of Molecular Sciences 20, no. 20 (October 21, 2019): 5222. http://dx.doi.org/10.3390/ijms20205222.
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In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.
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Dick, Jeffrey M. "Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress." PeerJ 5 (June 6, 2017): e3421. http://dx.doi.org/10.7717/peerj.3421.
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The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreasedZCor ${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$ of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package,canprot.
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Kuo, Ming-Tse, Po-Chiung Fang, Shu-Fang Kuo, Alexander Chen, and Yu-Ting Huang. "Tear Proteomics Study of Dry Eye Disease: Which Eye Do You Adopt as the Representative Eye for the Study?" International Journal of Molecular Sciences 22, no. 1 (January 3, 2021): 422. http://dx.doi.org/10.3390/ijms22010422.
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Most studies about dry eye disease (DED) chose unilateral eye for investigation and drew conclusions based on monocular results, whereas most studies involving tear proteomics were based on the results of pooling tears from a group of DED patients. Patients with DED were consecutively enrolled for binocular clinical tests, tear biochemical markers of DED, and tear proteome. We found that bilateral eyes of DED patients may have similar but different ocular surface performance and tear proteome. Most ocular surface homeostatic markers and tear biomarkers were not significantly different in the bilateral eyes of DED subjects, and most clinical parameters and tear biomarkers were correlated significantly between bilateral eyes. However, discrepant binocular presentation in the markers of ocular surface homeostasis and the associations with tear proteins suggested that one eye’s performance cannot represent that of the other eye or both eyes. Therefore, in studies for elucidating tear film homeostasis of DED, we may lose some important messages hidden in the fellow eye if we collected clinical and proteomic data only from a unilateral eye. For mechanistic studies, it is recommended that researchers collect tear samples from the eye with more severe DED under sensitive criteria for identifying the more severe eye and evaluating the tear biochemical and proteomic markers with binocular concordance drawn in prior binocular studies.
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Marques, Isabel, Duarte Gouveia, Jean-Charles Gaillard, Sónia Martins, Magda C. Semedo, Fernando C. Lidon, Fábio M. DaMatta, Ana I. Ribeiro-Barros, Jean Armengaud, and José C. Ramalho. "Next-Generation Proteomics Reveals a Greater Antioxidative Response to Drought in Coffea arabica Than in Coffea canephora." Agronomy 12, no. 1 (January 8, 2022): 148. http://dx.doi.org/10.3390/agronomy12010148.
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Drought is a major threat to coffee, compromising the quality and quantity of its production. We have analyzed the core proteome of 18 Coffea canephora cv. Conilon Clone 153 and C. arabica cv. Icatu plants and assessed their responses to moderate (MWD) and severe (SWD) water deficits. Label-free quantitative shotgun proteomics identified 3000 proteins in both genotypes, but less than 0.8% contributed to ca. 20% of proteome biomass. Proteomic changes were dependent on the severity of drought, being stronger under SWD and with an enrolment of different proteins, functions, and pathways than under MWD. The two genotypes displayed stress-responsive proteins under SWD, but only C. arabica showed a higher abundance of proteins involved in antioxidant detoxification activities. Overall, the impact of MWD was minor in the two genotypes, contrary to previous studies. In contrast, an extensive proteomic response was found under SWD, with C. arabica having a greater potential for acclimation/resilience than C. canephora. This is likely supported by a wider antioxidative response and an ability to repair photosynthetic structures, being crucial to develop new elite genotypes that assure coffee supply under water scarcity levels.
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Rahman, Md Saidur, June-Sub Lee, Woo-Sung Kwon, and Myung-Geol Pang. "Sperm Proteomics: Road to Male Fertility and Contraception." International Journal of Endocrinology 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/360986.
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Spermatozoa are highly specialized cells that can be easily obtained and purified. Mature spermatozoa are transcriptionally and translationally inactive and incapable of protein synthesis. In addition, spermatozoa contain relatively higher amounts of membrane proteins compared to other cells; therefore, they are very suitable for proteomic studies. Recently, the application of proteomic approaches such as the two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in-gel electrophoresis has identified several sperm-specific proteins. These findings have provided a further understanding of protein functions involved in different sperm processes as well as of the differentiation of normal state from an abnormal one. In addition, studies on the sperm proteome have demonstrated the importance of spermatozoal posttranslational modifications and their ability to induce physiological changes responsible for fertilization. Large-scale proteomic studies to identify hundreds to thousands of sperm proteins will ultimately result in the development of novel biomarkers that may help to detect fertility, the state of complete contraception, and beyond. Eventually, these protein biomarkers will allow for a better diagnosis of sperm dysfunctions and aid in drug development. This paper reviews the recent scientific publications available from the PubMed database to address sperm proteomics and its potential application to characterize male fertility and contraception.
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Poulsen, T. B. G., J. S. Andersen, M. K. Kristiansen, S. Rasmusen, L. Arent-Nielsen, C. H. Nielsen, and A. Stensballe. "AB1254 PHENOTYPING OF MULTIPLE BIOFLUIDS FOR LIQUID BIOMARKERS FOR DIAGNOSTICS AND PERSONALIZED MEDICINE OF RHEUMATOID ARTHRITIS, SPONDYLOARTHRITIS AND OSTEOARTHRITIS." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 1918.1–1919. http://dx.doi.org/10.1136/annrheumdis-2020-eular.5949.
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Background:Inflammatory and autoimmune diseases include multifactual pathomechanisms and systemic responses. The etiology of the joint diseases rheumatoid arthritis (RA), spondyloarthritis (SpA) in relation to osteoarthritis (OA) remain incomplete and establishing the correct diagnose remains nontrivial. Advances in high-throughput molecular technologies have increased investigations into the utility of transcriptomic, proteomic and high-density protein arrays approaches as diagnostic tools and companion diagnostics for precision medicine. To increase our understanding of the molecular pathogenesis, we extracted synovial fluid from the joints from multiple patient groups and characterized the protein composition in relation to plasma. Basic blood tests include inflammatory markers and autoantibodies, however, now analysis speed and robustness allow more readily clinical insight biofluids.Objectives:We present recent Omics concepts and studies investigating inflammatory state and treatment outcome in different biofluids from plasma to synovial fluid accessing causalities leading to inflammation and pain. Additionally, the aim was to investigate in any proteomic findings in synovial fluid can be correlated to proteomic changes in patient plasma and can be used as biomarkers for treatment effect.Methods:Plasma and synovial fluid were investigated in multiple pathologies before and after treatment in patients (biologics; MTX; intraarticular gold). Deep proteome, PTM and EV profiling were accomplished using quantitative proteomics approaches using quantitative mass spectrometry-based analysis by DIA/PASEF followed by deep datamining. All biological samples were digested according to a Filter Aided Sample Preparation (FASP) protocol before analysis with tandem mass spectrometry (MS/MS). PTM profiling were evaluated by 4D CCS based feature finding.Results:Mass spectrometry based profiling allowed quantitative profiling of up to 480 proteins in matched synovial fluid and plasma. Complementary analysis by Olink proteomics, cytokine profiling and cell-free DNA. Multiple acute inflammatory proteins were more abundant in the RA synovial fluid, including proteins originating from neutrophil granulocytes, whereas SpA patients had a higher concentration of haptoglobin. Complementary analysis by Olink immunoassay identified significantly downregulated inflammation markers out of 96 tested in relation to antiinflammatory treatment.Conclusion:Discovery of biomarkers and/or inflammatory signatures through integration of multi-omic data allowed stratify patients for improved treatment and prognosis. Firstly, our data using next generation proteomics approaches alleviates many pitfalls of missing values and poor proteome coverage including unbiased PTM profiling without enrichment strategies.Disclosure of Interests:None declared
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Dubin, Ruth F., and Eugene P. Rhee. "Proteomics and Metabolomics in Kidney Disease, including Insights into Etiology, Treatment, and Prevention." Clinical Journal of the American Society of Nephrology 15, no. 3 (October 21, 2019): 404–11. http://dx.doi.org/10.2215/cjn.07420619.
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In this review of the application of proteomics and metabolomics to kidney disease research, we review key concepts, highlight illustrative examples, and outline future directions. The proteome and metabolome reflect the influence of environmental exposures in addition to genetic coding. Circulating levels of proteins and metabolites are dynamic and modifiable, and thus amenable to therapeutic targeting. Design and analytic considerations in proteomics and metabolomics studies should be tailored to the investigator’s goals. For the identification of clinical biomarkers, adjustment for all potential confounding variables, particularly GFR, and strict significance thresholds are warranted. However, this approach has the potential to obscure biologic signals and can be overly conservative given the high degree of intercorrelation within the proteome and metabolome. Mass spectrometry, often coupled to up-front chromatographic separation techniques, is a major workhorse in both proteomics and metabolomics. High-throughput antibody- and aptamer-based proteomic platforms have emerged as additional, powerful approaches to assay the proteome. As the breadth of coverage for these methodologies continues to expand, machine learning tools and pathway analyses can help select the molecules of greatest interest and categorize them in distinct biologic themes. Studies to date have already made a substantial effect, for example elucidating target antigens in membranous nephropathy, identifying a signature of urinary peptides that adds prognostic information to urinary albumin in CKD, implicating circulating inflammatory proteins as potential mediators of diabetic nephropathy, demonstrating the key role of the microbiome in the uremic milieu, and highlighting kidney bioenergetics as a modifiable factor in AKI. Additional studies are required to replicate and expand on these findings in independent cohorts. Further, more work is needed to understand the longitudinal trajectory of select protein and metabolite markers, perform transomics analyses within merged datasets, and incorporate more kidney tissue–based investigation.
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FOSTER, LEONARD J. "MASS SPECTROMETRY OUTGROWS SIMPLE BIOCHEMISTRY: NEW APPROACHES TO ORGANELLE PROTEOMICS." Biophysical Reviews and Letters 01, no. 02 (April 2006): 209–21. http://dx.doi.org/10.1142/s1793048006000057.
Full textAbstract:
Organelles are subcellular compartments or structures that typically carry out a defined set of functions within the cell. The functions of many organelles are known or predicted, but without knowing all the components of any recognized organelle it is difficult to fully understand them. Mass spectrometry-based proteomics now allows for routine identification of several hundreds or thousands of proteins in very complex samples; for cell biologists, organelles represent perhaps the most interesting class of cellular components to apply this new technology to. However, in order to analyze the proteome of an organelle it first must be purified, and the limitations in purifying any biological sample to homogeneity quickly become apparent to the vigilant mass spectrometrist. At the end of an organelle proteomic investigation, investigators are left with a long list of proteins whose location needs to be verified by an orthogonal method, a daunting prospect; or, they must accept an unknown and possibly very high level of incorrect localizations. Some of these caveats can be partially overcome by incorporating quantitative aspects into organelle proteomic studies. This review discusses some alternative approaches to organelle proteomics where questions of specificity and/or functional relevance are addressed by incorporating a quantitative dimension into the experiment.
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Le, Vu Anh, Cam Quyen Thi Phan, and Thuy Huong Nguyen. "Data mining in mass spectrometry-based proteomics studies." Science & Technology Development Journal - Engineering and Technology 2, no. 4 (March 24, 2020): 258–76. http://dx.doi.org/10.32508/stdjet.v2i4.483.
Full textAbstract:
The post-genomic era consists of experimental and computational efforts to meet the challenge of clarifying and understanding the function of genes and their products. Proteomic studies play a key role in this endeavour by complementing other functional genomics approaches, encompasses the large-scale analysis of complex mixtures, including the identification and quantification of proteins expressed under different conditions, the determination of their properties, modifications and functions. Understanding how biological processes are regulated at the protein level is crucial to understanding the molecular basis of diseases and often highlights the prevention, diagnosis and treatment of diseases. High-throughput technologies are widely used in proteomics to perform the analysis of thousands of proteins. Specifically, mass spectrometry (MS) is an analytical technique for characterizing biological samples and is increasingly used in protein studies because of its targeted, nontargeted, and high performance abilities. However, as large data sets are created, computational methods such as data mining techniques are required to analyze and interpret the relevant data. More specifically, the application of data mining techniques in large proteomic data sets can assist in many interpretations of data; it can reveal protein-protein interactions, improve protein identification, evaluate the experimental methods used and facilitate the diagnosis and biomarker discovery. With the rapid advances in mass spectrometry devices and experimental methodologies, MS-based proteomics has become a reliable and necessary tool for elucidating biological processes at the protein level. Over the past decade, we have witnessed a great expansion of our knowledge of human diseases with the adoption of proteomic technologies based on MS, which leads to many interesting discoveries. Here, we review recent advances of data mining in MS-based proteomics in biomedical research. Recent research in many fields shows that proteomics goes beyond the simple classification of proteins in biological systems and finally reaches its initial potential – as an essential tool to aid related disciplines, notably biomedical research. From here, there is great potential for data mining in MS-based proteomics to move beyond basic research, into clinical research and diagnostics.
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Castagnola, M., E. Scarano, G. C. Passali, I. Messana, T. Cabras, F. Iavarone, G. Di Cintio, A. Fiorita, E. De Corso, and G. Paludetti. "Salivary biomarkers and proteomics: future diagnostic and clinical utilities." Acta Otorhinolaryngologica Italica 37, no. 2 (April 2017): 94–101. http://dx.doi.org/10.14639/0392-100x-1598.
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Lo studio della proteomica salivare, test economico e non invasivo, rappresenta una fonte di numerose informazioni, ed è utile per la diagnosi di svariate malattie. Da quando siamo entrati nellera della tecnologia genomica e delle scienze omiche, la raccolta di campioni salivari è aumentata esponenzialmente. Recenti piattaforme proteomiche hanno analizzato il proteoma salivare umano, caratterizzando circa 3000 peptidi e proteine, espressi in maniera differente: più del 90% in peso deriva dalla secrezione delle tre ghiandole salivari maggiori, mentre la restante parte proviene dalle ghiandole salivari minori, dal fluido crevicolare gengivale, da essudati mucosi e dalla microflora orale. Lobiettivo principale dellanalisi proteomica è discriminare tra condizioni fisiologiche e patologiche. Ad oggi, tuttavia, non esiste un preciso protocollo che permetta di analizzare lintero proteoma salivare, pertanto sono state realizzate svariate strategie. Innanzitutto, è possibile distinguere due tipologie di piattaforme proteomiche: lapproccio top-down prevede lanalisi delle proteine sotto esame come entità intatte; nellapproccio bottom-up la caratterizzazione della proteina avviene mediante lo studio dei peptidi ottenuti dopo digestione enzimatica (con tripsina tipicamente). A causa di questa eterogeneità, per una stessa patologia sono stati proposti differenti biomarkers. Il proteoma salivare è stato caratterizzato in numerose malattie: carcinoma squamoso e leucoplachie orali, malattia del trapianto contro lospite (GVHD) cronica, sindrome di Sjögren e altri disordini autoimmuni come la sindrome SAPHO (sinovite, acne, pustolosi, iperostosi e osteite), schizofrenia e disordine bipolare, malattie genetiche come la sindrome di Down o la malattia di Wilson. In conclusione, i risultati delle ricerche riportate in questa review suggeriscono che nel prossimo futuro la saliva diverrà un fluido di indubbia rilevanza diagnostica utile per fini clinici, sia diagnostici, sia prognostici.
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Rodrigues, Joao E., Ana Martinho, Vítor Santos, Catia Santa, Nuno Madeira, Maria J. Martins, Carlos N. Pato, Antonio Macedo, and Bruno Manadas. "Systematic Review and Meta-Analysis on MS-Based Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Bipolar Disorder." International Journal of Molecular Sciences 23, no. 10 (May 13, 2022): 5460. http://dx.doi.org/10.3390/ijms23105460.
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Bipolar disorder (BD) is a clinically heterogeneous condition, presenting a complex underlying etiopathogenesis that is not sufficiently characterized. Without molecular biomarkers being used in the clinical environment, several large screen proteomics studies have been conducted to provide valuable molecular information. Mass spectrometry (MS)-based techniques can be a powerful tool for the identification of disease biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids to assess BD biomarkers and identify relevant networks of biological pathways. Following PRISMA guidelines, we searched for studies using MS proteomics to identify proteomic differences between BD patients and healthy controls (PROSPERO database: CRD42021264955). Fourteen articles fulfilled the inclusion criteria, allowing the identification of 266 differentially expressed proteins. Gene ontology analysis identified complement and coagulation cascades, lipid and cholesterol metabolism, and focal adhesion as the main enriched biological pathways. A meta-analysis was performed for apolipoproteins (A-I, C-III, and E); however, no significant differences were found. Although the proven ability of MS proteomics to characterize BD, there are several confounding factors contributing to the heterogeneity of the findings. In the future, we encourage the scientific community to use broader samples and validation cohorts, integrating omics with bioinformatics tools towards providing a comprehensive understanding of proteome alterations, seeking biomarkers of BD, and contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis.
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Cutillas, Pedro, Alma Burlingame, and Robert Unwin. "Proteomic Strategies and Their Application in Studies of Renal Function." Physiology 19, no. 3 (June 2004): 114–19. http://dx.doi.org/10.1152/nips.01515.2003.
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Proteomics is a promising new tool for functional genomics. In addition to two-dimensional gel electrophoresis, other methods that are based on liquid chromatography and mass spectrometry are now available to study proteins. In this brief article, we review the strengths and limitations of the proteomic approaches currently available to the researcher, and we provide examples of how proteomics has been, and can in the future be, used to study the kidney.