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Expert Review of Proteomics

Juan J Calvete
Venoms are integrated phenotypes used by a wide range of organisms for predatory and defensive purposes. The study of venoms is of great interest in diverse fields, such as evolutionary ecology and biotechnology. Omics technologies have contributed to understanding the evolutionary mechanisms that molded snake venoms to their present-day structural and functional variability lanscape. Areas covered: This review article reflects on two recent implementations in venomics: absolute quantification of intact proteins by elemental mass spectrometry, and top-down molecular mass spectrometry...
July 13, 2018: Expert Review of Proteomics
Yuanhui Ma, John R Yates
Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully-labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs)...
July 13, 2018: Expert Review of Proteomics
Arada Vinaiphat, Visith Thongboonkerd
Knowledge of the function of molecular chaperones is required for a better understanding of cellular proteostasis. Nevertheless, such information is currently dispersed as most of previous studies investigated chaperones on a single-angle basis. Recently, a new subdiscipline of chaperonology, namely 'chaperonomics' (defined as "systematic analysis of chaperone genes, transcripts, proteins, or their interaction networks using omics technologies"), has been emerging to better understand biological, physiological and pathological roles of chaperones...
July 13, 2018: Expert Review of Proteomics
Christian Delles, Emma Carrick, Delyth Graham, Stuart A Nicklin
Hypertension is a complex and multifactorial cardiovascular disorder. With different mechanisms contributing to a different extent to an individual's blood pressure, the discovery of novel pathogenetic principles of hypertension is challenging. However, there is an urgent and unmet clinical need to improve prevention, detection, and therapy of hypertension in order to reduce the global burden associated with hypertension-related cardiovascular diseases. Areas covered: Proteomic techniques have been applied in reductionist experimental models including angiotensin II infusion models in rodents and the spontaneously hypertensive rat in order to unravel mechanisms involved in blood pressure control and end organ damage...
July 12, 2018: Expert Review of Proteomics
Anna Psaroulaki, Dimosthenis Chochlakis
No abstract text is available yet for this article.
July 12, 2018: Expert Review of Proteomics
Anna Mantsiou, Antonia Vlahou, Jerome Zoidakis
Prostate cancer (PCa) is one of the leading causes of death in the male population worldwide. Various clinical samples such as urine, blood serum and prostatic fluid have been commonly used for the identification of PCa-associated molecular changes. Tissue, the site of oncogenesis, is increasingly gaining more attention as a study material for studies aimed at the discovery of biomarkers for predicting the disease outcome and therapeutic targets. Areas covered: This review is the output of a systematic literature search on PubMed to retrieve articles relevant to the proteomic analysis of tissues for the study of prostate cancer...
June 25, 2018: Expert Review of Proteomics
Shichen Shen, Xue Wang, Benjamin C Orsburn, Jun Qu
No abstract text is available yet for this article.
June 17, 2018: Expert Review of Proteomics
Fieke W Hoff, Chenyue W Hu, Amina A Qutub, Eveline S J M de Bont, Terzah M Horton, Steven M Kornblau
Although cure rates for acute leukemia have steadily improved over the past decades, leukemia remains a deadly disease. Enhanced risk stratification and new therapies are needed to improve outcome. Extensive genetic analyses have identified many mutations that contribute to the development of leukemia. However, most mutations occur infrequently and most gene alterations have been difficult to target. Most patients have more than one driver mutation in combination with secondary mutations, that result in a leukemic transformation via the alteration of proteins...
June 14, 2018: Expert Review of Proteomics
Ruzanna Mnatsakanyan, Gerta Shema, Mark Basik, Gerald Batist, Christoph H Borchers, Albert Sickmann, René P Zahedi
Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information - e.g., changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics) - holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading...
June 12, 2018: Expert Review of Proteomics
Hassan Dihazi, Abdul R Asif, Tim Beißbarth, Rainer Bohrer, Kirstin Feussner, Ivo Feussner, Olaf Jahn, Christof Lenz, Andrzej Majcherczyk, Bernhard Schmidt, Kerstin Schmitt, Henning Urlaub, Oliver Valerius
Multi-omic approaches are promising a broader view on cellular processes and a deeper understanding of biological systems. with strongly improved high-throughput methods the amounts of data generated have become huge, and their handling challenging. Area Covered: New bioinformatic tools and pipelines for the integration of data from different omics disciplines continue to emerge, and will support scientists to reliably interpret data in the context of biological processes. comprehensive data integration strategies will fundamentally improve systems biology and systems medicine...
May 18, 2018: Expert Review of Proteomics
Erica Gianazza, Cristina Banfi
Post-translational modifications (PTMs) have an important role in the regulation of protein function, localization, and interaction with other molecules. PTMs apply a dynamic control of proteins in both physiological and pathological conditions. The study of disease-specific PTMs allows identifying potential biomarkers and developing effective drugs. Enrichment techniques combined with high-resolution mass spectrometry (MS)/MS analysis provide attractive results on PTM characterization. Selected reaction monitoring/multiple reaction monitoring (SRM/MRM) is a powerful targeted assay for the quantitation and validation of PTMs in complex biological samples...
June 2018: Expert Review of Proteomics
Christina Looße, Frauke Swieringa, Johan W M Heemskerk, Albert Sickmann, Christin Lorenz
Platelets are the smallest cells within the circulating blood with key roles in physiological hemostasis and pathological thrombosis regulated by the onset of activating/inhibiting processes via receptor responses and signaling cascades. Areas covered: Proteomics as well as genomic approaches have been fundamental in identifying and quantifying potential targets for future diagnostic strategies in the prevention of bleeding and thrombosis, and uncovering the complexity of platelet functions in health and disease...
June 2018: Expert Review of Proteomics
Rohitesh Gupta, Moorthy P Ponnusamy
Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin...
June 2018: Expert Review of Proteomics
Suresh Gadher, Mangesh Bhide, Hana Kovarova
The Central and Eastern European Proteomic Conference (CEEPC) successfully launched its second decade of proteomics in Košice, Slovakia with a program of systems biology, cellular, clinical, veterinary and sports proteomics. Whilst many conferences are struggling to attract participants, CEEPC with its outstanding track record and unique 'family - feel' packaged with excellent ambiance is thriving and bringing together proteomics experts from academia, industry, scientific specialties, clinics and precision medicine communities interested in resolving mysteries about protein functionalities in health and disease...
May 2018: Expert Review of Proteomics
Shyam Sundar, Bhawana Singh
Leishmania spp. are causative agents of leishmaniasis, a broad-spectrum neglected vector-borne disease. Genomic and transcriptional studies are not capable of solving intricate biological mysteries, leading to the emergence of proteomics, which can provide insights into the field of parasite biology and its interactions with the host. Areas covered: The combination of genomics and informatics with high throughput proteomics may improve our understanding of parasite biology and pathogenesis. This review analyses the roles of diverse proteomic technologies that facilitate our understanding of global protein profiles and definition of parasite development, survival, virulence and drug resistance mechanisms for disease intervention...
May 2018: Expert Review of Proteomics
David J Harvey
Viral diseases contribute much to human and animal suffering and enormous efforts are directed at developing appropriate vaccines for protection. Glycoproteins constitute much of the viral surfaces and are obvious targets for such vaccine development. This review describes mass spectrometric methods used for the structural determination of these compounds. Areas covered: The review describes the structures of the N- and O-linked glycans found on glycoproteins and mass spectrometric methods for their ionization and fragmentation...
May 2018: Expert Review of Proteomics
Deepali Rathore, Anneliese Faustino, John Schiel, Eric Pang, Michael Boyne, Sarah Rogstad
Mass spectrometry (MS) is widely used in the characterization of biomolecules including peptide and protein therapeutics. These biotechnology products have seen rapid growth over the past few decades and continue to dominate the global pharmaceutical market. Advances in MS instrumentation and techniques have enhanced protein characterization capabilities and supported an increased development of biopharmaceutical products. Areas covered: This review describes recent developments in MS-based biotherapeutic analysis including sequence determination, post-translational modifications (PTMs) and higher order structure (HOS) analysis along with improvements in ionization and dissociation methods...
May 2018: Expert Review of Proteomics
Janine Naß, Thomas Efferth
INTRODUCTION: Cancer is one of the leading causes of morbidity and mortality worldwide. A hallmark of cancer is evasion of apoptosis leading to tumor progression and drug resistance. Biomarker research has become a sign of the times, and proteins involved in apoptosis may be used for clinical diagnostic or prognostic purposes in cancer treatment. The recent progress in proteomic technology has triggered an emerging number of researchers to study the molecular mechanisms that regulate the apoptotic signal transduction pathways in cancer...
May 2018: Expert Review of Proteomics
Stefania Mondello, Eric P Thelin, Gerry Shaw, Michel Salzet, Carmela Visalli, Dasa Cizkova, Firas Kobeissy, Andras Buki
Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. Accurate classification according to injury-specific and patient-specific characteristics is critical to help informed clinical decision-making and to the pursuit of precision medicine in TBI. Reliable biomarker signatures for improved TBI diagnostics are required but still an unmet need. Areas covered: Extracellular vesicles (EVs) represent a new class of biomarker candidates in TBI. These nano-sized vesicles have key roles in cell signaling profoundly impacting pathogenic pathways, progression and long-term sequelae of TBI...
May 2018: Expert Review of Proteomics
Mustapha Benkhalifa, Yosra Zayani, Véronique Bach, Henri Copin, Moncef Feki, Moncef Benkhalifa, Monia Allal-Elasmi
The progress in in vitro fertilization (IVF) techniques for infertility management has led to the investigation of embryo implantation site proteins such as Matrix metalloproteinases (MMPs), which may have a key role in embryo-endometrium crosstalk and in the molecular mechanisms of the embryo implantation. Areas covered: Numerous studies have generated much information concerning the relation between the different proteins at the site of implantation such as cytokines, growth factors, adhesion molecules and MMPs...
April 2018: Expert Review of Proteomics
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