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Journal of Proteomics

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https://www.readbyqxmd.com/read/28634120/highly-reproducible-improved-label-free-quantitative-analysis-of-cellular-phosphoproteome-by-optimization-of-lc-ms-ms-gradient-and-analytical-column-construction
#1
Nagib Ahsan, Judson Belmont, Zhuo Chen, James G Clifton, Arthur R Salomon
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634119/an-ultrasensitive-stain-for-negative-protein-detection-in-sds-page-via-4-5-dibromofluorescein
#2
Dongdong Yu, Yang Wang, Shaoqing Zhang, Zhiwei Chen, Mei Xue, Ying Wang, Weitao Cong, Litai Jin, Zhongxin Zhu
A highly sensitive method for brief and economical staining of proteins in 1-D and 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) by 4',5'-Dibromofluorescein (DBF) was developed in this study. Down to 0.025-0.05ng protein could be detected within 10min (only 2 steps) by DBF stain, which is approximately 10-fold more sensitive than those of Eosin Y (EY) and SYPRO Ruby stains, and 20-fold more sensitive than that of imidazole-zinc (IZ) negative stain. In addition, the LC-MS/MS results indicated that the newly developed staining method is compatible with the downstream protein identification...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634118/identification-of-chickpea-seed-proteins-resistant-to-simulated-in-vitro-human-digestion
#3
I C Ribeiro, C C Leclercq, N Simões, A Toureiro, I Duarte, J B Freire, M M Chaves, J Renaut, C Pinheiro
Proteins and peptides able to resist gastrointestinal digestion and reach the intestinal mucosa have the potential to influence human health. Chickpea (Cicer arietinum L.) seed proteins are able to resist cooking (86.9% total protein) and/or in vitro simulated human digestion (15.9% total protein resists soaking, cooking and digestion with pepsin and pancreatin). To identify and characterize proteins resisting digestion we made use of different MS methodologies. The efficiency of several proteases (trypsin, AspN, chymotrypsin and LysC) was tested, and two technologies were employed (MALDI-TOF-TOF and LC-nESI-MS/MS)...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28629798/proteomic-analysis-of-mesenchymal-to-schwann-cell-transdifferentiation
#4
Anup D Sharma, Jayme Wiederin, Metin Uz, Pawel Ciborowski, Surya K Mallapragada, Howard E Gendelman, Donald S Sakaguchi
While transplantation of Schwann cells facilitates axon regeneration, remyelination and repair after peripheral nerve injury clinical use is limited by cell bioavailability. We posit that such limitation in cell access can be overcome by the use of autologous bone-marrow derived mesenchymal stem cells (MSCs). As MSCs can transdifferentiate to Schwann cell-phenotypes and accelerate nerve regeneration we undertook proteomic evaluation of the cells to uncover the protein contents that affects Schwann cell formulation...
June 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28625740/comparative-proteomic-analysis-of-two-transgenic-low-gliadin-wheat-lines-and-non-transgenic-wheat-control
#5
María Dolores García-Molina, Vera Muccilli, Rosaria Saletti, Salvatore Foti, Stefania Masci, Francisco Barro
Gluten proteins are major determinants of the bread making quality of wheat, but also of important wheat-related disorders, including coeliac disease (CD), and allergies. We carried out a proteomic study using the total grain proteins from two low-gliadin wheat lines, obtained by RNAi, and the untransformed wild type as reference. The impact of silencing on both target and on non-target proteins was evaluated. Because of the great protein complexity, we performed separate analyses of four kernel protein fractions: gliadins and glutenin subunits, and metabolic and CM-like proteins, by using a classical 2D electrophoresis gel based approach followed by RP-HPLC/nESI-MS/MS...
June 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28625739/changes-in-the-fine-root-proteome-of-fagus-sylvatica-l-trees-associated-with-p-deficiency-and-amelioration-of-p-deficiency
#6
Christoph-Martin Geilfus, Sebastien Christian Carpentier, Aljoša Zavišić, Andrea Polle
Phosphorus is often the least available macronutrient in soil. Lack in phosphorus has detrimental effect on growth and biomass production of European Fagus sylvatica L., a major trees species in temperate forests. In contrast to leaf tissues, few studies have examined changes in the root system and no study has ever investigated the proteomic changes affected in beech roots by a lack in available phosphate (P). Here, we studied roots of young Fagus sylvatica L. trees in their native soils from two forests sites with contrasting availability of P: one P rich and P poor soil...
June 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28624520/dissecting-the-chloroplast-proteome-of-chickpea-cicer-arietinum-l-provides-new-insights-into-classical-and-non-classical-functions
#7
Nilesh Vikram Lande, Pratigya Subba, Pragya Barua, Dipak Gayen, T S Keshava Prasad, Subhra Chakraborty, Niranjan Chakraborty
Chloroplast, the energy organelle unique to plant cells, is a dynamic entity which integrates an array of metabolic pathways and serves as first level for energy conversion for the entire ecological hierarchy. Increasing amount of sequence data and evolution of mass spectrometric approaches has opened up new avenues for opportune exploration of the global proteome of this organelle. In our study, we aimed at generation of a comprehensive catalogue of chloroplast proteins in a grain legume, chickpea and provided a reference proteome map...
June 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28624519/itraq-based-quantitative-proteomics-analysis-of-molecular-mechanisms-associated-with-bombyx-mori-lepidoptera-larval-midgut-response-to-bmnpv-in-susceptible-and-near-isogenic-strains
#8
Haizhong Yu, Xueyang Wang, Jiaping Xu, Yan Ma, Shangzhi Zhang, Dong Yu, Dongqiong Fei, Azharuddin Muhammad
Bombyx mori nucleopolyhedrovirus (BmNPV) has been identified as a major pathogen responsible for severe economic loss. Most silkworm strains are susceptible to BmNPV, with only a few highly resistant strains thus far identified. Here we investigated the molecular basis of silkworm resistance to BmNPV using susceptible (the recurrent parent P50) and resistant (near-isogenic line BC9) strains and a combination of iTRAQ-based quantitative proteomics, reverse-transcription quantitative PCR and Western blotting...
June 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28627465/differential-proteome-analysis-of-hippocampus-and-temporal-cortex-using-label-free-based-2d-lc-ms-ms
#9
Xiaoyan Liu, Zhengguang Guo, Wei Liu, Wei Sun, Chao Ma
Hippocampus and temporal cortex are important brain regions, which play distinct, but complimentary roles in mediating learning and memory. Herein, we utilized label-free differential proteome strategy to explore function of normal human hippocampus and temporal cortex in learning and memory. As a result, a total of 5529 and 5702 proteins were identified in hippocampus and temporal cortex, respectively, 516 of which were significantly differential expressed, with abundance span 5 orders of magnitudes. Pathways analysis showed that temporal cortex was involved in growth of axons growth and synapse density regulation, through which could regulate long-term potentiation and long-term retention of trace memory...
June 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28627464/analysis-of-protein-complexes-in-arabidopsis-leaves-using-size-exclusion-chromatography-and-label-free-protein-correlation-profiling
#10
Uma K Aryal, Zachary McBride, Donglai Chen, Jun Xie, Daniel B Szymanski
Protein complexes are fundamentally important for diverse cellular functions, and create functionalities that could never be achieved by a single polypeptide. Knowledge of the protein complex assemblies that exist in plant cells are limited. To close this gap, we applied an integrative proteomic approach that combines cell fractionation, protein chromatography and quantitative mass spectrometry (MS) to analyze the oligomerization state of thousands of proteins in a single experiment. Soluble extracts from intact Arabidopsis leaves were fractionated using size exclusion chromatography (SEC), and abundance profiles across the column fractions were quantified using label-free precursor ion (MS1) intensity...
June 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28610761/comparative-proteomic-analysis-provides-insight-into-the-biological-role-of-protein-phosphatase-inhibitor-2-from-arabidopsis
#11
Nagib Ahsan, Mingjie Chen, Fernanda Salvato, Rashaun S Wilson, R Shyama Prasad Rao, Jay J Thelen
Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes...
June 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28602982/mass-spectrometry-based-shiga-toxin-identification-an-optimized-approach
#12
Keding Cheng, Angela Sloan, Xingle Li, Glen D Armstrong, Gehua Wang
Toxin expression is a key factor in Shiga toxin (Stx)-producing E. coli, a common pathogen involved in foodborne disease outbreaks. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) based approach has been used in this study to identify commonly reported E. coli toxins, with a focus on Shiga toxins (Stxs). Different sample preparation methods using variable culture conditions and concentrations of mitomycin C (MMC), a common antibiotic/chemotherapy agent capable of stimulating Stx production, were first tested on reference strains EDL933 and 90-2380 by LC-MS/MS detection of tryptic digests of receptor-analogue affinity binding enriched Stx preparations from culture supernatants and lysates...
June 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28602553/proteomic-profiling-of-the-brain-of-mice-with-experimental-cerebral-malaria
#13
Ehab Moussa, Honglei Huang, Malika Ahras, Amar Lall, Marie L Thezenas, Roman Fischer, Benedikt M Kessler, Arnab Pain, Oliver Billker, Climent Casals-Pascual
Cerebral malaria (CM) is a severe neurological complication of malaria infection in both adults and children. In pursuit of effective treatment of CM, clinical studies, postmortem analysis and animal models have been employed to understand the pathology and identify effective interventions. In this study, a shotgun proteomics analysis was conducted to profile the proteomic signature of the brain tissue of mice with experimental cerebral malaria (ECM) in order to further understand the underlying pathology. To identify CM-associated response, proteomic signatures of the brains of C57/Bl6N mice infected with P...
June 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28602552/intensity-fading-maldi-tof-mass-spectrometry-and-functional-proteomics-assignments-to-identify-protease-inhibitors-in-marine-invertebrates
#14
Giovanni Covaleda, Sebastian A Trejo, Emir Salas-Sarduy, Maday Alonso Del Rivero, Maria Angeles Chavez, Francesc X Aviles
Proteases and their inhibitors have become molecules of increasing fundamental and applicative value. Here we report an integrated strategy to identify and analyze such inhibitors from Caribbean marine invertebrates extracts by a fast and sensitive functional proteomics-like approach. The strategy works in three steps: i) multiplexed enzymatic inhibition kinetic assays, ii) Intensity Fading MALDI-TOF MS to establish a link between inhibitory molecules and the related MALDI signal(s) detected in the extract(s), and iii) ISD-CID-T(3) MS fragmentation on the parent MALDI signals selected in the previous step, enabling the partial or total top-down sequencing of the molecules...
June 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28583384/hydrocarbon-induced-changes-in-proteins-and-fatty-acids-profiles-of-raoultella-ornithinolytica-m03
#15
A Zdarta, J Tracz, M Luczak, U Guzik, E Kaczorek
Microorganisms can support environmental restoration by biodegradation of hydrocarbons but the mechanism of this process has been not described in detail yet. We present the effect of benzene derivatives on Raoultella ornithinolytica M03 cell composition. Comparison of the cell response after short-term and long-term stress revealed significant differences in surface properties, fatty acid composition and proteins profile. R. ornithinolytica M03 after long-term stress was characterized by lower cell surface hydrophobicity and much higher inner membrane permeability...
June 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28577918/the-neuropeptidome-of-the-crown-of-thorns-starfish-acanthaster-planci
#16
Meaghan K Smith, Tianfang Wang, Saowaros Suwansa-Ard, Cherie A Motti, Abigail Elizur, Min Zhao, Matthew L Rowe, Michael R Hall, Maurice R Elphick, Scott F Cummins
Outbreaks of Crown-of-Thorns Starfish (COTS; Acanthaster planci) are a major cause of destruction of coral communities on the Australian Great Barrier Reef. While factors relating to population explosions and the social interactions of COTS have been well studied, little is known about the neural mechanisms underlying COTS physiology and behaviour. One of the major classes of chemical messengers that regulate physiological and behavioural processes in animals is the neuropeptides. Here, we have analysed COTS genome and transcriptome sequence data to identify neuropeptide precursor proteins in this species...
May 31, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28571969/proteomic-fingerprinting-of-mistletoe-viscum-album-l-via-combinatorial-peptide-ligand-libraries-and-mass-spectrometry-analysis
#17
María Vergara-Barberán, María Jesús Lerma-García, Maria Nicoletti, Ernesto Francisco Simó-Alfonso, José Manuel Herrero-Martínez, Elisa Fasoli, Pier Giorgio Righetti
Combinatorial peptide ligand libraries (CPLLs), coupled to mass spectrometry (MS) analysis, have been used to investigate in depth the proteome of Viscum album L. (VA), commonly named European mistletoe, in order to provide a first proteomic fingerprinting. For this purpose, the proteins were captured via CPLLs at two different pH values (acidic and neutral). A total of 648 non-redundant proteins were identified by using two different databases. The two pH values, chosen for bead incubations, have contributed to increment the capture ability: 56% and 31% of CPLLs species were respectively recognized at pH7...
May 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28571968/determination-of-the-protein-expression-profiles-of-propsilocerus-akamusi-tokunaga-malpighian-tubules-response-to-cadmium-stress-by-itraq-coupled-lc-ms-ms
#18
Xianyun Zheng, Zhiying Xie, Shu Wang, Pipeng Lin
Propsilocerus akamusi (Tokunaga) is an important prey species for fish and aquatic birds, which represent an important link in the aquatic food chain as other species of Chironomidae. Malpighian tubules (MT) play an important role in metabolism and detoxification of harmful compounds and metal accumulation. Our previous studies have reported that P. akamusi have an extraordinary resistance to Cd. In this paper, iTRAQ-based proteomics technology was first used to study the differential proteomics of MT of Propsilocerus akamusi under sublethal Cd stress for different time courses...
May 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28554670/serine-protease-isoforms-in-gloydius-intermedius-venom-full-sequences-molecular-phylogeny-and-evolutionary-implications
#19
Zhang-Min Yang, Hui Yu, Zhen-Zhen Liu, Jian-Zhu Pei, Yu-E Yang, Su-Xian Yan, Cui Zhang, Wen-Long Zhao, Zhe-Zhi Wang, Ying-Ming Wang, Inn-Ho Tsai
Nine distinct venom serine proteases (vSPs) of Gloydius intermedius were studied by transcriptomic, sub-proteomic and phylogenetic analyses. Their complete amino acid sequences were deduced after Expression Sequence Tag (EST) analyses followed by cDNA cloning and sequencing. These vSPs appear to be paralogs and contain the catalytic triads and 1-4 potential N-glycosylation sites. Their relative expression levels evaluated by qPCR were grossly consistent with their EST hit-numbers. The major vSPs were purified by HPLC and their N-terminal sequences matched well to the deduced sequences, while fragments of the minor vSPs were detected by LC-MS/MS identification...
May 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28552833/wheat-glutenin-the-tail-of-the-1by-protein-subunits
#20
Júlio D Nunes-Miranda, Emmanuelle Bancel, Didier Viala, Christophe Chambon, José L Capelo, Gérard Branlard, Catherine Ravel, Gilberto Igrejas
Gluten-forming storage proteins play a major role in the viscoelastic properties of wheat dough through the formation of a continuous proteinaceous network. The high-molecular-weight glutenin subunits represent a functionally important subgroup of gluten proteins by promoting the formation of large glutenin polymers through interchain disulphide bonds between glutenin subunits. Here, we present evidences that y-type glutenin subunits encoded at the Glu-B1 locus are prone to proteolytic processing at the C-terminus tail, leading to the loss of the unique cysteine residue present at the C-terminal domain...
May 25, 2017: Journal of Proteomics
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