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proteomics and visualization

Stanislav Naryzhny
The main intricacy in the human proteome is that it is tremendously complex and composed from diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances in the technology of so called "Top-Down" mass spectrometry based proteomics, have been made. However, the scale of performance of this approach is still far behind the "Bottom-Up", peptide-centric techniques...
May 16, 2018: Journal of Proteomics
Narek Darabedian, Jinxu Gao, Kelly N Chuh, Christina M Woo, Matthew R Pratt
Metabolic chemical reporters of glycosylation in combination with bioorthogonal reactions have been known for two decades and have been used by many different research labs for the identification and visualization of glycoconjugates. More recently, however, they have begun to see utility for the investigation of cellular metabolism and the tolerance of biosynthetic enzymes and glycosyltransferases to dif-ferent sugars. Here, we take this concept one step further by using the metabolic chemical reporter 6-azido-6-deoxy-glucose (6AzGlc)...
May 17, 2018: Journal of the American Chemical Society
Pallab Bhowmick, Yassene Mohammed, Christoph H Borchers
Motivation: Multiple Reaction Monitoring (MRM)-based targeted proteomics is increasingly being used to study the molecular basis of disease. When combined with an internal standard, MRM allows absolute quantification of proteins in virtually any type of sample but the development and validation of an MRM assay for a specific protein is laborious. Therefore, several public repositories now host targeted proteomics MRM assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker, with all of which contain different levels of information...
May 14, 2018: Bioinformatics
Rashmi Madda, Shih-Chang Lin, Wei-Hsin Sun, Shir-Ly Huang
Context: Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease with unknown etiology. Objective: Human plasma is comprised of over 10 orders of magnitude concentration of proteins and tissue leakages. The changes in the abundance of these proteins have played an important role in various human diseases. Therefore, the research objective of this study is to identify the significantly altered expression levels of plasma proteins from SLE patients compared with healthy controls using proteomic analysis...
2018: PeerJ
Yanyun Wang, Haibo Luo, Guanglu Che, Yanqin Li, Jun Gao, Qiongli Yang, Bin Zhou, Linbo Gao, Tao Wang, Yujie Liang, Lin Zhang
Premature rupture of membranes (PROM) is a common pregnancy complication that frequently results in maternal and perinatal morbidity. The present methods for diagnosing PROM do not satisfy clinical requirements. The present study aimed to examine the proteome profile of amniotic fluid (AF) and maternal plasma, screen unique proteins in AF, and evaluate their diagnostic value for diagnosing PROM. The proteome profiles of AF and maternal plasma were examined via liquid chromatography coupled with tandem mass spectrometry‑based proteomic techniques...
May 3, 2018: Molecular Medicine Reports
Lars Kolbowski, Colin Combe, Juri Rappsilber
We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts...
May 8, 2018: Nucleic Acids Research
Bedilu Allo, Xudong Lou, Alexandre Bouzekri, Olga I Ornatsky
Mass cytometry is a highly multiplexed single-cell analysis platform that uses metal tagged reagents to identify multiple cellular biomarkers. Current metal-tagged reagent preparation employs thiol-maleimide chemistry to covalently couple maleimide-functionalized metal-chelating polymers (MCPs) with antibodies (Abs), a process that requires partial reduction of the Ab to form reactive thiol groups. However, some classes of Abs (for example, IgM) as well as biomolecules lacking cysteine residues has been challenging to label using this method...
May 7, 2018: Bioconjugate Chemistry
Dan Wang, Yong Sun, Lili Chang, Zheng Tong, Quanliang Xie, Xiang Jin, Liping Zhu, Peng He, Hongbin Li, Xuchu Wang
Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species...
May 3, 2018: Journal of Proteomics
Marcin Poreba, Wioletta Rut, Matej Vizovisek, Katarzyna Groborz, Paulina Kasperkiewicz, Darren Finlay, Kristiina Vuori, Dusan Turk, Boris Turk, Guy S Salvesen, Marcin Drag
Cysteine cathepsins normally function in the lysosomal degradation system where they are critical for the maintenance of cellular homeostasis and the MHC II immune response, and have been found to have major roles in several diseases and in tumor progression. Selective visualization of individual protease activity within a complex proteome is of major importance to establish their roles in both normal and tumor cells, thereby facilitating our understanding of the regulation of proteolytic networks. A generally accepted means to monitor protease activity is the use of small molecule substrates and activity-based probes...
February 28, 2018: Chemical Science
Nicola Bordin, Juan Carlos González-Sánchez, Damien P Devos
Interest in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum is growing within the microbiology community. These organisms do not have a specialized web resource that gathers in silico predictions in an integrated fashion. Hence, we are providing the PVC community with PVCbase, a specialized web resource that gathers in silico predictions in an integrated fashion. PVCbase integrates protein function annotations obtained through sequence analysis and tertiary structure prediction for 39 representative PVC proteomes (PVCdb), a protein feature visualizer (Foundation) and a custom BLAST webserver (PVCBlast) that allows to retrieve the annotation of a hit directly from the DataTables...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Zaver M Bhujwalla, Samata Kakkad, Zhihang Chen, Jiefu Jin, Sudath Hapuarachchige, Dmitri Artemov, Marie-France Penet
Most diseases, especially cancer, would significantly benefit from precision medicine where treatment is shaped for the individual. The concept of theragnostics or theranostics emerged around 2002 to describe the incorporation of diagnostic assays into the selection of therapy for this purpose. Increasingly, theranostics has been used for strategies that combine noninvasive imaging-based diagnostics with therapy. Within the past decade theranostic imaging has transformed into a rapidly expanding field that is located at the interface of diagnosis and therapy...
April 25, 2018: Journal of Magnetic Resonance
Qionger He, Erica D Arroyo, Samuel N Smukowski, Jian Xu, Claire Piochon, Jeffrey N Savas, Carlos Portera-Cailliau, Anis Contractor
Sensory perturbations in visual, auditory and tactile perception are core problems in fragile X syndrome (FXS). In the Fmr1 knockout mouse model of FXS, the maturation of synapses and circuits during critical period (CP) development in the somatosensory cortex is delayed, but it is unclear how this contributes to altered tactile sensory processing in the mature CNS. Here we demonstrate that inhibiting the juvenile chloride co-transporter NKCC1, which contributes to altered chloride homeostasis in developing cortical neurons of FXS mice, rectifies the chloride imbalance in layer IV somatosensory cortex neurons and corrects the development of thalamocortical excitatory synapses during the CP...
April 27, 2018: Molecular Psychiatry
Keli Hočevar, Aleš Maver, Tanja Kunej, Borut Peterlin
Sarcoidosis is a multifactorial systemic disease characterized by granulomatous inflammation and greatly impacting on global public health. The etiology and mechanisms of sarcoidosis are not fully understood. Recent high-throughput biological research has generated vast amounts of multi-omics big data on sarcoidosis, but their significance remains to be determined. We sought to identify novel candidate regions, and genes consistently altered in heterogeneous omics studies so as to reveal the underlying molecular mechanisms...
April 24, 2018: Omics: a Journal of Integrative Biology
Lei Wei, Jesse G Meyer, Birgit Schilling
Post-translational modification (PTM) of protein lysine residues by NƐ-acylation induces structural changes that can dynamically regulate protein functions, for example, by changing enzymatic activity or by mediating interactions. Precise quantification of site-specific protein acylation occupancy, or stoichiometry, is essential for understanding the functional consequences of both global low-level stoichiometry and individual high-level acylation stoichiometry of specific lysine residues. Other groups have reported measurement of lysine acetylation stoichiometry by comparing the ratio of peptide precursor isotopes from endogenous, natural abundance acylation and exogenous, heavy isotope-labeled acylation introduced after quantitative chemical acetylation of proteins using stable isotope-labeled acetic anhydride...
April 4, 2018: Journal of Visualized Experiments: JoVE
Lev I Levitsky, Mark V Ivanov, Anna A Lobas, Julia A Bubis, Irina A Tarasova, Elizaveta M Solovyeva, Marina L Pridatchenko, Mikhail V Gorshkov
We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel ``auto-tune'' feature, IdentiPy outperforms the popular alternatives on high-resolution data sets...
April 23, 2018: Journal of Proteome Research
Daniel Niedieker, Frederik Großerüschkamp, Anja Schreiner, Katalin Barkovits, Carsten Kötting, Katrin Marcus, Klaus Gerwert, Matthias Vorgerd
INTRODUCTION: The aim of this study was the label-free identification of distinct myopathological features with coherent anti-Stokes Raman scattering (CARS) imaging, which leaves the sample intact for further analysis. METHODS: The protein distribution was determined without labels by CARS at 2930 cm-1 and was compared with the results of standard histological staining. RESULTS: CARS imaging enabled the visualization of glycogen accumulation in glycogen storage disease type 5 (McArdle) and of internal nuclei in centronuclear myopathy...
April 16, 2018: Muscle & Nerve
Xianquan Zhan, Yuda Huang, Ying Long
Human pituitary adenoma (PA) is a common tumor that occurs in the human pituitary gland in the hypothalamus-pituitary-targeted organ axis systems, and may be classified as either clinically functional or nonfunctional PA (FPA and NFPA). NFPA is difficult for early stage diagnosis and therapy due to barely elevating hormones in the blood compared to FPA. Our long-term goal is to use proteomics methods to discover reliable biomarkers for clarification of PA molecular mechanisms and recognition of effective diagnostic, prognostic markers and therapeutic targets...
April 2, 2018: Journal of Visualized Experiments: JoVE
Katarína Furmanová, Jan Byška, Eduard M Gröller, Ivan Viola, Jan J Paleček, Barbora Kozlíková
BACKGROUND: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space...
April 6, 2018: BMC Bioinformatics
Alex X Lu, Yolanda T Chong, Ian Shen Hsu, Bob Strome, Louis-Francois Handfield, Oren Kraus, Brenda J Andrews, Alan M Moses
Evaluating protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation and more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern...
April 5, 2018: ELife
Jose Bonilla, Valerie Ryan, Gamze Yazar, Jozef L Kokini, Arun K Bhunia
The importance of gluten proteins, gliadins and glutenins, is well known in the quality of wheat products. In order to gain more specific information about the role of glutenins in wheat dough the two major subunits of glutenin, high and low molecular weight (HMW and LMW) glutenins were extracted, isolated and identified by mass spectrometry. Antibodies for HMW and LMW glutenins were developed using the proteomic information of the characterized glutenin subunits. The antibodies were found to be specific to each subunit by western immunoblots and were then conjugated to Quantum Dots using site click conjugation a new method to keep antibodies integrity...
April 4, 2018: Journal of Agricultural and Food Chemistry
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