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Proteomics

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https://www.readbyqxmd.com/read/28816396/identification-of-novel-site-specific-alterations-in-the-modification-level-of-myelin-basic-protein-isolated-from-mouse-brain-at-different-ages-using-capillary-electrophoresis-mass-spectrometry
#1
Bettina Sarg, Klaus Faserl, Herbert H Lindner
Myelin basic protein (MBP) is a multifunctional protein involved in maintaining the stability and integrity of the myelin sheath by a variety of interactions with membranes and other proteins. MBP is subjected to extensive post-translational modifications (PTMs) that are known to be crucial for the regulation of these interactions. Here we report capillary electrophoresis-mass spectrometric (CE-MS) analysis for the separation and identification of MBP peptides that incorporate the same PTM at different sites, creating multiple localization variants, and the ability to analyze challenging modifications such as asparagine and glutamine deamidation, isomerization and arginine citrullination...
August 17, 2017: Proteomics
https://www.readbyqxmd.com/read/28815942/plasma-membrane-protein-profiling-in-beta-amyloid-treated-microglia-cell-line
#2
Virginia Correani, Laura Di Francesco, Giuseppina Mignogna, Cinzia Fabrizi, Stefano Leone, Alessandra Giorgi, Alessia Passeri, Roberto Casata, Lorenzo Fumagalli, Bruno Maras, M Eugenia Schininà
In the responsiveness of microglia to toxic stimuli, plasma membrane proteins play a key role. In this study we treated with a synthetic beta amyloid peptide murine microglial cells metabolically differently labelled with stable isotope amino acids (SILAC). The plasma membrane was selectively enriched by a multi-stage aqueous two-phase partition system. We were able to identify by 1D-LC-MS/MS analyses 1577 proteins, most of them are plasma membrane proteins according to the Gene Ontology annotation. An unchanged level of amyloid receptors in this data set, suggests that microglia preserve their responsiveness capability to the environment even after 24 h-challenge with amyloid peptides...
August 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28792687/ols-client-and-ols-dialog-open-source-tools-to-annotate-public-omics-datasets
#3
Yasset Perez-Riverol, Tobias Ternent, Maximilian Koch, Harald Barsnes, Olga Vrousgou, Simon Jupp, Juan Antonio Vizcaíno
The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language (OWL)-based ontologies, among many other improvements...
August 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28792668/comparative-transcriptomic-and-proteomic-analyses-reveal-a-flug-mediated-signalling-pathway-relating-to-asexual-sporulation-of-antrodia-camphorata
#4
Hua-Xiang Li, Zhen-Ming Lu, Qing Zhu, Jin-Song Gong, Yan Geng, Jin-Song Shi, Zheng-Hong Xu, Yan-He Ma
Medicinal mushroom Antrodia camphorata sporulate large numbers of arthroconidia in submerged fermentation, which is rarely reported in basidiomycetous fungi. Nevertheless, the molecular mechanisms underlying this asexual sporulation (conidiation) remain unclear. Here, we used comparative transcriptomic and proteomic approaches to elucidate possible signalling pathway relating to the asexual sporulation of A. camphorata. First, 104 differentially expressed proteins and 2586 differential cDNA sequences during the culture process of A...
August 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28782881/from-peptide-masses-to-pregnancy-maintenance-a-comprehensive-proteomic-analysis-of-the-early-equine-embryo-secretome-blastocoel-fluid-and-capsule
#5
Aleona Swegen, Christopher Gerald Grupen, Zamira Gibb, Mark Baker, Marta de Ruijter-Villani, Nathan Druery Smith, Tom A E Stout, R John Aitken
Early pregnancy in the mare is a poorly understood, high risk period during which the embryo communicates its presence to the maternal endometrium. Remarkably, the maternal recognition of pregnancy signal is unknown in the horse. This study aimed to profile the proteins secreted by equine blastocysts into their immediate environment, along with proteins contained in the blastocoel and within the acellular embryo capsule. Embryos were recovered on day 8 after ovulation and cultured for 48 hours. Secretomes of day 9 and day 10 embryos were analyzed by LC-MS/MS and supported by analysis of blastocoel fluid and embryo capsule...
August 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28776938/hpslpred-an-ensemble-multi-label-classifier-for-human-protein-subcellular-location-prediction-with-imbalanced-source
#6
Shixiang Wan, Yucong Duan, Quan Zou
Predicting the subcellular localization of proteins is an important and challenging problem. Traditional experimental approaches are often expensive and time-consuming. Consequently, a growing number of research efforts employ a series of machine learning approaches to predict the subcellular location of proteins. There are two main challenges among the state-of-the-art prediction methods. First, most of the existing techniques are designed to deal with multi-class rather than multi-label classification, which ignores connections between multiple labels...
August 4, 2017: Proteomics
https://www.readbyqxmd.com/read/28771958/divergent-proteome-patterns-of-egg-albumen-from-domestic-chicken-duck-goose-turkey-quail-and-pigeon
#7
Congjiao Sun, Junnian Liu, Wenbo Li, Guiyun Xu, Ning Yang
To uncover a diversity of genetic and biological unknowns, a comprehensive and comparative proteomic analysis was performed on egg albumen of domestic chicken, duck, goose, turkey, quail and pigeon with tandem mass tags (TMTs) quantification technology. In this study, a total of 148, 138, 150, 162, 183 and 179 proteins were identified in egg albumen of the above six species respectively. Venn plots, PCA and cluster analysis all revealed the highest similarity of protein composition between duck and goose (∼75%)...
August 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28771929/comparative-itraq-based-quantitative-proteomic-analysis-of-pelteobagrus-vachelli-liver-against-acute-hypoxia-implications-in-metabolic-responses
#8
Guosong Zhang, Jiajia Zhang, Xin Wen, Cheng Zhao, Hongye Zhang, Xinru Li, Shaowu Yin
More and more frequently these days, aquatic ecosystems are being stressed by nutrient enrichment, pollutants, and global warming, leading to a serious depletion in oxygen concentrations. Although a sudden, significant lack of oxygen will result in mortality, fishes can have an acute behaviour (e.g., an increase in breathing rate, reduction in swimming frequency) and physiology responses (e.g., increase in oxygen delivery, and reduction in oxygen consumption) to hypoxia, which allows them to maintain normal physical activity...
August 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28762254/the-effects-of-prenatal-iron-deficiency-and-risperidone-treatment-on-the-rat-frontal-cortex-%C3%A2-a-proteomic-analysis
#9
Lorna Farrelly, Maria Victoria Rosato-Siri, Melanie Föcking, Martin Codagnone, Analia Reines, Patrick Dicker, Kieran Wynne, Michael Farrell, Mary Cannon, Gerard Cagney, Juana Maria Pasquini, David R Cotter
Prenatal iron deficiency (pID) has been described to increase the risk for neurodevelopmental disorders such as autism and schizophrenia; however, the precise molecular mechanisms are still unknown. Here, we utilized high throughput mass spectrometry to examine the proteomic effects of pID in adulthood on the rat frontal cortex area (FCA). In addition, the FCA proteome was examined in adulthood following risperidone treatment in adolescence to see if these effects could be prevented. We identified 1501 proteins of which 100 were significantly differentially expressed in the FCA at post-natal day 90...
July 31, 2017: Proteomics
https://www.readbyqxmd.com/read/28759167/titsmall-but-mighty-functional-peptides-encoded-by-small-orfs-in-plants
#10
REVIEW
Polly Yingshan Hsu, Philip N Benfey
Peptides encoded by small open reading frames (sORFs, usually < 100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from non-translated ones. Here we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics...
July 31, 2017: Proteomics
https://www.readbyqxmd.com/read/28755400/mapping-the-in-vitro-interactome-of-cardiac-sodium-na-calcium-ca-2-exchanger-1-ncx1
#11
Tandekile Lubelwana Hafver, Pimthanya Wanichawan, Ornella Manfra, Gustavo Antonio de Souza, Marianne Lunde, Marita Martinsen, William Edward Louch, Ole Mathias Sejersted, Cathrine Rein Carlson
NCX1 is an antiporter membrane protein encoded by the SLC8A1 gene. In the heart, it maintains cytosolic Ca(2+) homeostasis, serving as the primary mechanism for Ca(2+) extrusion during relaxation. Dysregulation of NCX1 is observed in end-stage human heart failure. In this study we used affinity purification coupled with mass spectrometry in rat left ventricle lysates to identify novel NCX1 interacting proteins in the heart. Two screens were conducted using: 1) anti-NCX1 against endogenous NCX1 and 2) anti-His with His-TF-NCX1cyt recombinant protein as bait...
July 28, 2017: Proteomics
https://www.readbyqxmd.com/read/28727291/proteomic-analysis-and-bioluminescent-reporter-gene-assays-to-investigate-effects-of-simulated-microgravity-on-caco-2-cells
#12
Giorgia La Barbera, Anna Laura Capriotti, Elisa Michelini, Susy Piovesana, Maria Maddalena Calabretta, Riccardo Zenezini Chiozzi, Aldo Roda, Aldo Laganà
Microgravity is one of the most important features in spaceflight. Previous evidence from in-vitro studies has shown that significant changes occur under simulated microgravity. For this reason, human colon adenocarcinoma Caco-2 cells were selected as cell model of intestinal epithelial barrier and their response to altered gravity conditions was investigated, especially on the protein level. In this study, we combined label-free shotgun proteomics and bioluminescent reporter gene assays to identify key proteins and pathways involved in the response of Caco-2 cells under reference and microgravity conditions...
July 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28722797/highly-selective-enrichment-of-phosphopeptides-by-on-chip-indium-oxide-functionalized-magnetic-nanoparticles-coupled-with-maldi-tof-ms
#13
Dandan Jiang, Naizhong Song, Xiqian Li, Jiutong Ma, Qiong Jia
Selective and efficient preconcentration is indispensable for low concentration of phosphopeptides in phosphorylated protein-related samples prior to MS-based analysis. Herein, an on-chip system coupled magnetic SPE with MALDI-TOF MS was designed. A metal oxide affinity chromatography (MOAC) material, indium oxide, was coated on the surface of Fe3 O4 magnetic nanoparticles (MNPs) to prepare the adsorbent, spatially confined with an applied magnetic field. The adsorbent exhibited high selectivity for phosphopeptides in tryptic digests of the mixture of β-casein and BSA (1:1000) and the mixture of β-casein, BSA, and ovalbumin (1:100:100)...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28722786/oncogenic-transformation-of-lung-cells-results-in-distinct-exosome-protein-profile-similar-to-the-cell-of-origin
#14
Richard J Lobb, Marcus L Hastie, Emma L Norris, Rosa van Amerongen, Jeffrey J Gorman, Andreas Möller
Lung cancer is responsible for the highest rate of cancer mortality worldwide. Lung cancer patients are often ineligible for tumour biopsies due to co-morbidities. As a result, patients may not have the most effective treatment regimens administered. Patients with mutations in the epidermal growth factor receptor (EGFR) have improved survival in response to EGFR tyrosine kinase inhibitors (TKIs). A non-invasive method of determining EGFR mutations in patients would have promising clinical applications. Exosomes have the potential to be non-invasive novel diagnostic markers in cancer...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28722341/proteomic-analysis-of-neuroblastoma-derived-exosomes-new-insights-into-a-metastatic-signature
#15
Marta Colletti, Andrea Petretto, Angela Galardi, Virginia Di Paolo, Luigi Tomao, Chiara Lavarello, Elvira Inglese, Maurizio Bruschi, Ana Amor Lopez, Luisa Pascucci, Birgit Geoerger, Hector Peinado, Franco Locatelli, Angela Di Giannatale
Neuroblastoma (NB) is the most common extracranial pediatric solid tumor. Around 70% of patients with metastatic disease at diagnosis present bone-marrow infiltration, which is considered a marker of poor outcome; however, the mechanism underlying this specific tropism has to be elucidated. Tumor-derived exosomes may support metastatic progression in several tumors by interacting with the microenvironment, and may serve as tumor biomarkers. The main objective of this study was to identify an exosomal signature associated with NB metastatic bone-marrow dissemination...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28719092/what-is-targeted-proteomics-a-concise-revision-of-targeted-acquisition-and-targeted-data-analysis-in-mass-spectrometry
#16
Eva Borràs, Eduard Sabidó
No abstract text is available yet for this article.
July 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28714192/secreted-tumor-antigens-immune-biomarkers-for-diagnosis-and-therapy
#17
REVIEW
Els N Meeusen, Elgene Lim, Suresh Mathivanan
With the advent of immunotherapies for cancer, there is growing interest in the identification of tumor antigens. Tumor antigens are self-molecules altered through genetic mutations (neoantigens), protein truncation, protein misfolding or abnormal post translational modifications. To induce an immune response, tumor antigens need to be secreted into the tumor environment and presented to the immune system in the draining lymph nodes, resulting in the generation of tumor-specific effector cells and antibodies...
July 17, 2017: Proteomics
https://www.readbyqxmd.com/read/28686798/multiplierz-v2-0-a-python-based-ecosystem-for-shared-access-and-analysis-of-native-mass-spectrometry-data
#18
William M Alexander, Scott B Ficarro, Guillaume Adelmant, Jarrod A Marto
The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data...
July 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28665052/discovery-of-breast-putative-cancer-antigens-using-an-integrative-platform-of-genomics-driven-immunoproteomics
#19
Veneta Qendro, Deborah H Lundgren, Samuel Palczewski, Poornima Hegde, Christina Stevenson, Laurie Perpetua, Ardian Latifi, Jesse Merriman, Grace Bugos, David K Han
Recent advances in cancer immuno-therapeutics such as checkpoint inhibitors, chimeric antigen-receptor T cells, and tumor infiltrating T cells (TIL) are now significantly impacting cancer patients in a positive manner. Although very promising, reports indicate no more than 25% of cases result in complete remission. One of the limitations of these treatments is the identity of putative cancer antigens in each patient as it is technically challenging to identify of cancer antigens in a rapid fashion. Thus, identification of cancer antigens followed by targeted treatment will increase the efficacy of cancer immunotherapies...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28665046/features-of-lineage-specific-haematopoietic-metabolism-revealed-by-mitochondrial-proteomics
#20
Claudia Billing, Michael Walker, Nicole Noack, Christian Böhme, Uta Ceglarek, Dietger Niederwieser, Anthony Whetton, Michael Cross
Hematopoietic bone marrow is a regenerative tissue of high clinical relevance, yet relatively little is known about the metabolism of the stem and progenitor populations concerned. We have used a multipotent murine cell line to generate sufficient numbers of cells undergoing self-renewal, erythroid or myeloid differentiation to allow a proteomics analysis of enriched mitochondria. Stringent analysis identified 37 mitochondria-associated proteins changing on differentiation in this system. Those induced during differentiation were commonly associated with mature cell functions, while those inactivated upon differentiation indicate widespread changes in mitochondrial transport, fatty acid catabolism and oxidative phosphorylation...
June 30, 2017: Proteomics
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