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Journal of Proteomics

Kun Gao, Xiang-Yuan Deng, Meng-Ke Shang, Guang-Xing Qin, Cheng-Xiang Hou, Xi-Jie Guo
: Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) specifically infects the epithelial cells in the midgut of silkworm and causes them to death, which negatively affects the sericulture industry. In order to determine the midgut response at the protein levels to the virus infection, differential proteomes of the silkworm midgut responsive to BmCPV infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
November 28, 2016: Journal of Proteomics
Liang Song, Fei Wang, Zhaoming Dong, Xiaoting Hua, Qingyou Xia
: Paralytic peptide (PP) participates in diverse physiological processes as an insect cytokine, such as immunity control, paralysis induction, regulation of cell morphology and proliferation. To investigate the molecular mechanism underlying those physiological activities, we systematically investigated the global phosphorylation events in fat body of silkworm larvae induced by PP through label-free quantitative phosphoproteomics. 2534 phosphosites were finally identified, of which the phosphorylation level of 620 phosphosites on 244 proteins was significantly up-regulated and 67 phosphosites on 43 proteins was down-regulated...
November 26, 2016: Journal of Proteomics
Chengjian Tu, Shichen Shen, Quanhu Sheng, Yu Shyr, Jun Qu
: Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%...
November 26, 2016: Journal of Proteomics
Kaberi Datta, Trayambak Basak, Swati Varshney, Shantanu Sengupta, Sagartirtha Sarkar
: Myocardial infarction is one of the leading causes of cardiac dysfunction, failure and sudden death. Post infarction cardiac remodeling presents a poor prognosis, with 30%-45% of patients developing heart failure, in a period of 5-25years. Oxidative stress has been labelled as the primary causative factor for cardiac damage during infarction, however, the impact it may have during the process of post infarction remodeling has not been well probed. In this study, we have implemented iTRAQ proteomics to catalogue proteins and functional processes, participating both temporally (early and late phases) and spatially (infarct and remote zones), during post myocardial infarction remodeling of the heart as functions of the differential oxidative stress manifest during the remodeling process...
November 25, 2016: Journal of Proteomics
Franck Limonier, Katleen Van Steendam, Geneviève Waeterloos, Koen Brusselmans, Myriam Sneyers, Dieter Deforce
: Thromboembolic events (TEE) associated to trace amounts of plasmatic activated coagulation factor XI (FXIa) in administrated immunoglobulin (Ig) have recently raised concerns and hence there is a need for highly sensitive profiling of residual plasma source proteins. This study aims to consider LC-ESI-QTOF data-dependent acquisition in combination with sample fractionation for this purpose. Sample fractionation proved mandatory to enable identification of plasma residuals. Two approaches were compared: Ig depletion with protein G - protein A affinity chromatography and low-abundant protein enrichment with a combinatorial peptide ligand library (ProteoMiner(TM), Bio-Rad)...
November 25, 2016: Journal of Proteomics
Davide Chiasserini, Magdalena Davidescu, Pier Luigi Orvietani, Federica Susta, Lara Macchioni, Maya Petricciuolo, Emilia Castigli, Rita Roberti, Luciano Binaglia, Lanfranco Corazzi
: Glioblastoma (GBM) is the most common and aggressive brain tumours of adults. The metabolic phenotype of GBM cells is highly dependent on glycolysis; therefore, therapeutic strategies aimed at interfering with glycolytic pathways are under consideration. 3-Bromopyruvate (3BP) is a potent antiglycolytic agent, with a variety of targets and possible effects on global cell metabolism. Here we analyzed the changes in protein expression on a GBM cell line (GL15 cells) caused by 3BP treatment using a global proteomic approach...
November 23, 2016: Journal of Proteomics
Chih-Wei Liu, Lisa Bramer, Bobbie-Jo Webb-Robertson, Kathleen Waugh, Marian J Rewers, Qibin Zhang
Human blood plasma proteome reflects physiological changes associated with a child's development as well as development of disease states. While age-specific normative values are available for proteins routinely measured in clinical practice, there is paucity of comprehensive longitudinal data regarding changes in human plasma proteome during childhood. We applied TMT-10plex isobaric labeling-based quantitative proteomics to longitudinally profile the plasma proteome in 10 healthy children during their development, each with 9 serial time points from 9months to 15years of age...
November 23, 2016: Journal of Proteomics
Víctor Llombart, Sebastián Alejandro Trejo, Sílvia Bronsoms, Anna Morancho, Ma Feifei, Júlia Faura, Teresa García-Berrocoso, Alba Simats, Anna Rosell, Francesc Canals, Mar Hernández-Guillamón, Joan Montaner
: The identification of proteins involved in brain ischemia might allow the discovery of putative biomarkers or therapeutic targets for ischemic stroke. Our aim is to study the distribution of proteins within mouse brain after an ischemic insult using MALDI imaging-mass-spectrometry and to identify relevant proteins involved in brain damage. We occluded the middle cerebral artery of C57BL/6J mice. Brain slices were analyzed by MALDI-TOF and infarct (IC) and contralateral (CL) regions were compared using ClinProTools...
November 22, 2016: Journal of Proteomics
Paulo André Dias Bastos, João Pinto da Costa, Rui Vitorino
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health...
November 22, 2016: Journal of Proteomics
Estela Giménez, Marina Gay, Marta Vilaseca
: Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages...
November 17, 2016: Journal of Proteomics
Patricia Fernández-Puente, Valentina Calamia, Lucía González-Rodríguez, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Cristina Ruiz-Romero, Francisco J Blanco
: The methods currently available for the diagnosis and monitoring of osteoarthritis (OA) are very limited and lack sensitivity. Being the most prevalent rheumatic disease, one of the most disabling pathologies worldwide and currently untreatable, there is a considerable interest pointed in the verification of specific biological markers for improving its diagnosis and disease progression studies. Considering the remarkable development of targeted proteomics methodologies in the frame of the Human Proteome Project, the aim of this work was to develop and apply a MRM-based method for the multiplexed analysis of a panel of 6 biomarker candidates for OA encoded by the Chromosome 16, and another 8 proteins identified in previous shotgun studies as related with this pathology, in specimens derived from the human joint and serum...
November 16, 2016: Journal of Proteomics
Eoin Scanlan, Lu Yu, Duncan Maskell, Jyoti Choudhary, Andrew Grant
: Campylobacter jejuni is the leading cause of bacterial gastroenteritis in the world. A number of factors are believed to contribute to the ability of C. jejuni to cause disease within the human host including the secretion of non-flagellar proteins via the flagellar type III secretion system (FT3SS). Here for the first time we have utilised quantitative proteomics using stable isotope labelling by amino acids in cell culture (SILAC), and label-free liquid chromatography-mass spectrometry (LC/MS), to compare supernatant samples from C...
November 16, 2016: Journal of Proteomics
Min Zhang, Shou-Ting Cheng, Hai-Yun Wang, Jia-He Wu, Yuan-Ming Luo, Qian Wang, Fu-Xin Wang, Gui-Xian Xia
: The soil-borne necrotrophic pathogen fungus Rhizoctonia solani is destructive, causing disease in various important crops. To date, little is known about the host defence mechanism in response to invasion of R. solani. Here, an iTRAQ-based proteomic analysis was employed to investigate pathogen-responsive proteins in the disease tolerant/resistant cotton cultivar CRI35. A total of 174 differentially accumulated proteins (DAPs) were identified after inoculation of cotton plants with R...
November 15, 2016: Journal of Proteomics
Andrea Bileck, Rupert L Mayer, Dominique Kreutz, Tamara Weiss, Sabine Taschner-Mandl, Samuel M Meier, Astrid Slany, Christopher Gerner
: Peripheral blood mononuclear cells are important players in immune regulation relying on a complex network of signaling pathways. In this study, we evaluated the power of label-free quantitative shotgun proteomics regarding the comprehensive characterization of signaling pathways in such primary cells by studying regulation of protein abundance, post-translational modifications and nuclear translocation events. The effects of inflammatory stimulation and the treatment of stimulated cells with dexamethasone were investigated...
November 13, 2016: Journal of Proteomics
Raluca M Boteanu, Viorel I Suica, Elena Uyy, Luminita Ivan, Simona O Dima, Irinel Popescu, Maya Simionescu, Felicia Antohe
: There is a wide range of pathological conditions proved to be associated with inflammation. The inflammatory process offers protection against harmful stimuli such as induced cell injury and tissues damage by means of specialized mediators and cells. Alarmins, also known as endogenous danger signals or damage-associated molecular patterns (DAMPs) molecules, are critical players of immune response to tissue suffering. In many inflammatory and autoimmune conditions, alarmins are released into the extracellular milieu and bind to specific receptors to stimulate and promote activation of innate immune cells, cell differentiation, cell death or secretion of inflammatory mediators...
November 11, 2016: Journal of Proteomics
Milan Oldřich Urban, Jakub Vašek, Miroslav Klíma, Jana Krtková, Klára Kosová, Ilja Tom Prášil, Pavel Vítámvás
: The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders...
November 10, 2016: Journal of Proteomics
Robert Starke, Martina Müller, Michael Gaspar, Manja Marz, Kirsten Küsel, Kai Uwe Totsche, Martin von Bergen, Nico Jehmlich
: Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3μm glass filters. In total, 3808 protein groups were identified...
November 10, 2016: Journal of Proteomics
Kíssila Rabelo, Monique R O Trugilho, Simone M Costa, Bernardo A S Pereira, Otacílio C Moreira, André T S Ferreira, Paulo C Carvalho, Jonas Perales, Ada M B Alves
: Dengue is an important mosquito borne viral disease in the world. Dengue virus (DENV) encodes a polyprotein, which is cleaved in ten proteins, including the non-structural protein 1 (NS1). In this work, we analyzed the effect of NS1 expression in one hepatic cell line, HepG2, through a shotgun proteomic approach. Cells were transfected with pcENS1 plasmid, which encodes the DENV2 NS1 protein, or the controls pcDNA3 (negative control) and pMAXGFP (GFP, a protein unrelated to dengue)...
November 5, 2016: Journal of Proteomics
Wen Zhang, Ting Zhong, Yun Chen
: In breast cancer, p53 could be functionally compromised by interaction with several proteins. Among those proteins, MDM2 serves as a pivotal negative regulator and counteracts p53 activation. Thus, the ability to quantitatively and accurately monitor the changes in level of p53-MDM2 interaction with disease state can enable an improved understanding of this protein-protein interaction (PPI), provide a better insight into cancer development and allow the emergence of advanced treatments...
November 4, 2016: Journal of Proteomics
André M Almeida, Paolo Nanni, Ana M Ferreira, Claudia Fortes, Jonas Grossmann, Rui J B Bessa, Paulo Costa
Beef production is an important economic activity. In Southern Europe there are two types of beef production systems based on growth paths: continuous (CG) versus discontinuous growth (DG). DG is a traditional system dependent on pasture; whereas in CG animals are supplemented on concentrate feed. We compare the protein abundance profiles of the longissimus thoracis (LT) muscle in CG and DG animals using label-free quantitative proteomics. Twenty three Alentejana male calves (9months-old, 239kg live-weight) were allocated to two feeding regimens...
November 2, 2016: Journal of Proteomics
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