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Journal of Proteomics

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https://read.qxmd.com/read/30776456/optimisation-of-protein-extraction-for-in-depth-profiling-of-the-cereal-grain-proteome
#1
Utpal Bose, James A Broadbent, Keren Byrne, Shihab Hasan, Crispin A Howitt, Michelle L Colgrave
Cereal grain proteomics can provide valuable information regarding plant growth, nutritional status, adaptation to environmental stresses, and the role that grain proteins play in health disorders, such as coeliac disease. In this study liquid chromatography-mass spectrometry was used to compare the barley proteome after extraction using seven protocols, with and without defatting and protein precipitation steps that aimed to remove interfering secondary metabolites. Tris-HCl and urea buffers yielded 1405 and 1483 proteins (~79% overlap) from barley (cv Sloop)...
February 15, 2019: Journal of Proteomics
https://read.qxmd.com/read/30772490/quantitative-label-free-mass-spectrometry-using-contralateral-and-adjacent-breast-tissues-reveal-differentially-expressed-proteins-and-their-predicted-impacts-on-pathways-and-cellular-functions-in-breast-cancer
#2
Talita Helen Bombardelli Gomig, Iglenir João Cavalli, Ricardo Lehtonen Rodrigues de Souza, Evelyn Vieira, Aline Castro Rodrigues Lucena, Michel Batista, Kelly Cavalcanti Machado, Fabricio Klerynton Marchini, Fabio Albuquerque Marchi, Rubens Silveira Lima, Cícero de Andrade Urban, Luciane Regina Cavalli, Enilze Maria de Souza Fonseca Ribeiro
Proteins play an essential role in the biological processes associated with cancer. Their altered expression levels can deregulate critical cellular pathways and interactive networks. In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma...
February 14, 2019: Journal of Proteomics
https://read.qxmd.com/read/30763807/progress-in-farm-animal-proteomics-the-contribution-of-combinatorial-peptide-ligand-libraries
#3
Egisto Boschetti, Lorenzo E Hernández-Castellano, Pier Giorgio Righetti
The present review covers proteomics discoveries in farm animals using combinatorial peptide ligand libraries (CPLLs). These libraries enhance the identification of low-abundance proteins by compressing the dynamic range of the protein concentration. This technology can be applied in multiple biological fluids, such as plasma or serum, follicular and cerebrospinal fluids, urine, saliva, tears seminal fluid, milk whey and even lymph. The discovery of low-abundance proteins contributes to the continuous monitoring for animal pathologies, which allows early treatment and disease prevention...
February 11, 2019: Journal of Proteomics
https://read.qxmd.com/read/30763806/intact-protein-mass-spectrometry-reveals-intraspecies-variations-in-venom-composition-of-a-local-population-of-vipera-kaznakovi-in-northeastern-turkey
#4
Daniel Petras, Benjamin-Florian Hempel, Bayram Göçmen, Mert Karis, Gareth Whiteley, Simon C Wagstaff, Paul Heiss, Nicholas R Casewell, Ayse Nalbantsoy, Roderich D Süssmuth
We report on the variable venom composition of a population of the Caucasus viper (Vipera kaznakovi) in Northeastern Turkey. We applied a combination of venom gland transcriptomics, and de-complexing bottom-up and top-down venomics. In contrast to sole bottom-up venomics approaches and gel or chromatography based venom comparison, our combined approach enables a faster and more detailed comparison of venom proteomes from multiple individuals. In total, we identified peptides and proteins from 15 toxin families, including snake venom metalloproteinases (svMP; 37...
February 11, 2019: Journal of Proteomics
https://read.qxmd.com/read/30731211/integrative-analyses-of-myocardial-lipidome-and-proteome-implicate-mitochondrial-dysfunction-in-lethal-ventricular-tachyarrhythmia-lvta-induced-by-acute-myocardial-ischemia-ami
#5
Jiayan Wu, Yongping Zhang, Qian Wu, Dezhi Xie, Xiaojun Zhang, Dian Wang
Lethal ventricular tachyarrhythmia (LVTA) is the most prevalent electrophysiological event leading to sudden cardiac death (SCD). In this study, the myocardial lipidome and proteome were analysed in rats experiencing LVTA as a consequence of acute myocardial ischemia (AMI). Results showed that 257 lipid species and 814 myocardial proteins were disrupted during LVTA. Cardiolipin (CL), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ceramide (Cer), lysophosphatidylethanolamine (LPE), lysophosphatidylcholine (LPC), phosphatidylglycerol (PG), and lysophosphatidylserine (LPS) were down-regulated; whereas sphingosine (SO) and diacylglycerol (DG) were up-regulated...
February 4, 2019: Journal of Proteomics
https://read.qxmd.com/read/30731210/comparative-proteomics-and-metabolomics-of-jaz7-mediated-drought-tolerance-in-arabidopsis
#6
Li Meng, Tong Zhang, Sisi Geng, Peter B Scott, Haiying Li, Sixue Chen
Jasmonates (JAs) are important phytohormones that regulate a wide range of plant processes, including growth, development and stress responses. Jasmonate ZIM-domain (JAZ) proteins are transcriptional repressors in JA signaling. Overexpression of JAZ7 was found to confer drought tolerance in Arabidopsis thaliana (A. thaliana), but the molecular mechanisms are not known. Using Tandem Mass Tag (TMT) quantitative proteomics and targeted metabolomics approaches, we found that 394 unique proteins and 96 metabolites were differentially expressed under drought and/or among the three genotypes (wild type (WT), JAZ7 knock out (KO) and JAZ7 overexpression (OE))...
February 4, 2019: Journal of Proteomics
https://read.qxmd.com/read/30726703/itraq-based-analysis-of-leaf-proteome-identifies-important-proteins-in-secondary-metabolite-biosynthesis-and-defence-pathways-crucial-to-cross-protection-against-tmv
#7
Prem Prakash Das, Gao Ming Chua, Qingsong Lin, Sek-Man Wong
Cross-protection is a phenomenon in which infection with a mild virus strain protects host plants against subsequent infection with a closely related severe virus strain. This study showed that a mild strain mutant virus, Tobacco mosaic virus (TMV)-43A could cross protect Nicotiana benthamiana plants against wild-type TMV. Furthermore, we investigated the host responses at the proteome level to identify important host proteins involved in cross-protection. We used the isobaric tags for relative and absolute quantification (iTRAQ) technique to analyze the proteome profiles of TMV, TMV-43A and cross-protected plants at different time-points...
February 3, 2019: Journal of Proteomics
https://read.qxmd.com/read/30716422/mass-spectrometry-based-shiga-toxin-identification-a-clinical-validation
#8
Lijie Zhang, Lu Zhang, Yanhua Du, Xingle Li, Mark Unger, Derek Davlut, Angela Sloan, Glen D Armstrong, Gehua Wang, Keding Cheng
After we published our preliminary study on the use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and curated E. coli toxin databases on the identification of E. coli Shiga toxins (Stxs) in the Journal of Proteomics in year 2018, we were encouraged to further refine the method and test clinical isolates. In this study, different concentrations of mitomycin C (MMC) and ciprofloxacin (CF), two common antibiotic/chemotherapy agents capable of stimulating Stx production, were first tested and compared on three reference strains and eight clinical isolates to observe the toxin induction and subsequent identification...
February 1, 2019: Journal of Proteomics
https://read.qxmd.com/read/30710758/proteome-analysis-of-non-small-cell-lung-cancer-cell-line-secretomes-and-patient-sputum-reveals-biofluid-biomarker-candidates-for-cisplatin-response-prediction
#9
Franziska Böttger, Tieneke B M Schaaij-Visser, Inge de Reus, Sander R Piersma, Thang V Pham, Remco Nagel, Ruud H Brakenhoff, Erik Thunnissen, Egbert F Smit, Connie R Jimenez
Molecular markers are urgently needed to select non-small cell lung cancer (NSCLC) patients most likely to benefit from platinum-based chemotherapies. Of particular interest are proteins that can be found in biofluids like sputum for non-invasive detection. Therefore, we profiled the secretomes of 6 NSCLC cell lines with varying IC50-values for cisplatin, using label-free GeLC-MS/MS-based proteomics. Out of a total dataset of 2610 proteins, 304 proteins showed significant differences in expression levels between cisplatin sensitive and insensitive cell lines...
January 30, 2019: Journal of Proteomics
https://read.qxmd.com/read/30710757/univariate-and-classification-analysis-reveals-potential-diagnostic-biomarkers-for-early-stage-ovarian-cancer-type-1-and-type-2
#10
Simonas Marcišauskas, Benjamin Ulfenborg, Björg Kristjansdottir, Sofia Waldemarson, Karin Sundfeldt
Biomarkers for early detection of ovarian tumors are urgently needed. Tumors of the ovary grow within cysts and most are benign. Surgical sampling is the only way to ensure accurate diagnosis, but often leads to morbidity and loss of female hormones. The present study explored the deep proteome in well-defined sets of ovarian tumors, FIGO stage I, Type 1 (low-grade serous, mucinous, endometrioid; n = 9), Type 2 (high-grade serous; n = 9), and benign serous (n = 9) using TMT-LC-MS/MS. Data are available via ProteomeXchange with identifier PXD010939...
January 30, 2019: Journal of Proteomics
https://read.qxmd.com/read/30710756/molecular-pathways-of-varicocele-and-its-repair-a-paired-labelled-shotgun-proteomics-approach
#11
M Camargo, P Intasqui, L B Belardin, M P Antoniassi, K H M Cardozo, V M Carvalho, R Fraietta, R P Bertolla
Varicocelectomy is associated to improved semen quality and sperm functional quality, but individual response is highly variable. Thus, a prospective study was performed including 25 men who collected a semen sample before and 12 months after subinguinal microsurgical varicocelectomy. Semen analysis, sperm functional analysis, and seminal plasma proteomic analysis was performed before and 12 months after varicocelectomy, and according to improvement or not of semen quality (positive and negative outcome)...
January 30, 2019: Journal of Proteomics
https://read.qxmd.com/read/30707949/on-the-characterisation-of-the-porcine-gland-specific-salivary-proteome
#12
Sara Prims, Geert Van Raemdonck, Charlotte Vanden Hole, Steven Van Cruchten, Chris Van Ginneken, Xaveer Van Ostade, Christophe Casteleyn
To expand the knowledge on the porcine salivary proteome, secretions from the three major salivary glands were collected from anaesthetised piglets. Pilocarpine and isoproterenol were simultaneously injected intraperitoneally to increase the volume and protein concentration of the saliva, respectively. The protein composition and relative protein-specific abundance of saliva secreted by the parotid gland and by the mandibular and monostomatic sublingual gland, were determined using iTRAQ. When combining two detection methods, MALDI-TOF/TOF MS and Q-Exactive orbitrap MS/MS, a total of 122 porcine salivary proteins and 6 mammalian salivary proteins with a predicted porcine homolog were identified...
January 29, 2019: Journal of Proteomics
https://read.qxmd.com/read/30707948/sensitive-profiling-of-cell-surface-proteome-by-using-an-optimized-biotinylation-method
#13
Yanan Li, Yan Wang, Jiawei Mao, Yating Yao, Keyun Wang, Qinglong Qiao, Zheng Fang, Mingliang Ye
Cell surface proteins are responsible for many critical functions. Systematical profiling of these proteins would provide a unique molecular fingerprint to classify cells and provide important information to guide immunotherapy. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of cells...
January 29, 2019: Journal of Proteomics
https://read.qxmd.com/read/30677554/platelet-membrane-lipid-rafts-protein-composition-varies-following-gpvi-and-clec-2-receptors-activation
#14
Irene Izquierdo, María N Barrachina, Lidia Hermida-Nogueira, Vanessa Casas, Johannes A Eble, Montserrat Carrascal, Joaquín Abián, Ángel García
Lipid rafts are membrane microdomains that have been proposed to play an important role in several platelet-signalling cascades, including those mediated by the receptors Glycoprotein VI (GPVI), and C-type lectin domain family 1 member B (CLEC-2), both involved in thrombus formation. We have performed a LC-MS/MS proteomic analysis of lipid rafts isolated from platelets activated through GPVI and CLEC-2 as well as from resting platelets. Our aim was to determine the magnitude of changes in lipid rafts protein composition and to elucidate the relevance of these alterations in platelet function...
January 21, 2019: Journal of Proteomics
https://read.qxmd.com/read/30677553/molecular-characterization-and-in-vitro-interaction-analysis-of-op14-3-3-%C3%AE-protein-from-opuntia-ficus-indica-identification-of-a-new-client-protein-from-shikimate-pathway
#15
Eric E Hernández-Domínguez, Erandi Vargas-Ortiz, Esaú Bojórquez-Velázquez, Alberto Barrera-Pacheco, María S Santos-Díaz, Nancy G Camarena-Rangel, Ana P de la Barba Rosa
In plants, 14-3-3 proteins are important modulators of protein-protein interactions in response to environmental stresses. The aim of the present work was to characterize one Opuntia ficus-indica 14-3-3 and get information about its client proteins. To achieve this goal, O. ficus-indica 14-3-3 cDNA, named as Op14-3-3 μ, was amplified by 3'-RACE methodology. Op14-3-3 μ contains an Open Reading Frame of 786 bp encoding a 261 amino acids protein. Op14-3-3 μ cDNA was cloned into a bacterial expression system and recombinant protein was purified...
January 21, 2019: Journal of Proteomics
https://read.qxmd.com/read/30664952/itraq-based-quantitative-proteomics-analysis-of-the-spleen-reveals-innate-immunity-and-cell-death-pathways-associated-with-heat-stress-in-broilers-gallus-gallus
#16
Dandan Ma, Qingxiu Liu, Minhong Zhang, Jinghai Feng, Xiumei Li, Ying Zhou, Xuejie Wang
Heat stress induces immune dysfunction and cell death, but the mechanisms by which this occurs are not fully understood. Therefore, the isobaric tags for relative and absolute quantification (iTRAQ) was used to identify differentially abundant proteins (DAPs) in the spleen between heat-stressed group and control group, and real time qPCR (RT-qPCR), and Parallel Reaction Monitoring (PRM) were performed to validate the differentially abundant proteins of interest. The results showed that nine down regulated DAPs related to innate immunity were enriched in the Toll-like receptor signaling pathway (IRF3 and CD40), NOD-like receptor signaling pathway (TNFAIP3, IL-18, CathL2, IRF3, IAP3 and CYBA), RIG-I-like receptor signaling pathway (TRIM25 and IRF3), and Cytosolic DNA-sensing pathway (IL-18, POLR3F and IRF3)...
January 18, 2019: Journal of Proteomics
https://read.qxmd.com/read/30660770/a-large-scale-proteome-analysis-of-the-gefitinib-primary-resistance-overcome-by-kdac-inhibition-in-kras-mutated-adenocarcinoma-cells-overexpressing-amphiregulin
#17
Sylvia G Lehmann, Michel Seve, Laetitia Vanwonterghem, Sylvie Michelland, Valérie Cunin, Jean-Luc Coll, Amandine Hurbin, Sandrine Bourgoin-Voillard
KDAC inhibitors (KDACi) overcome gefitinib primary resistance in non-small cell lung cancer (NSCLC) including mutant-KRAS lung adenocarcinoma. To identify which proteins are involved in the restoration of this sensitivity and to provide new therapeutic targets for mutant-KRAS lung adenocarcinoma, we performed an iTRAQ quantitative proteomic analysis after subcellular fractionation of H358-NSCLC treated with gefitinib and KDACi (TSA/NAM) versus gefitinib alone. The 86 proteins found to have been significantly dysregulated between the two conditions, were mainly involved in cellular metabolism and cell transcription processes...
January 17, 2019: Journal of Proteomics
https://read.qxmd.com/read/30660769/high-resolution-quantitative-proteomics-applied-to-the-study-of-the-specific-protein-signature-in-the-sputum-and-saliva-of-active-tuberculosis-patients-and-their-infected-and-uninfected-contacts
#18
Jesús Mateos, Olivia Estévez, África González-Fernández, Luis Anibarro, Ángeles Pallarés, Rajko Reljic, José M Gallardo, Isabel Medina, Mónica Carrera
Our goal was to establish panels of protein biomarkers that are characteristic of patients with microbiologically confirmed pulmonary tuberculosis (TB) and their contacts, including latent TB-infected (LTBI) and uninfected patients. Since the first pathogen-host contact occurs in the oral and nasal passages the saliva and sputum were chosen as the biological fluids to be studied. Quantitative shotgun proteomics was performed using a LTQ-Orbitrap-Elite platform. For active TB patients, both fluids exhibited a specific accumulation of proteins that were related to complement activation, inflammation and modulation of immune response...
January 17, 2019: Journal of Proteomics
https://read.qxmd.com/read/30660768/quantitative-proteomics-reveals-systematic-dysregulations-of-liver-protein-metabolism-in-sucralose-treated-mice
#19
Chih-Wei Liu, Liang Chi, Pengcheng Tu, Jingchuan Xue, Hongyu Ru, Kun Lu
Sucralose, one kind of "sugar-free" artificial sweeteners, is widely used as food and drinks additives. It is generally considered that sucralose is safe because majority of ingested sucralose is not metabolized and absorbed by human body. However, increasing evidence shows the negative effects of artificial sweeteners in perturbations of gut microbiota which plays an important role in a variety of processes related to host health such as immune system development. Specifically, sucralose uptake can alter the homeostasis of mouse gut microbiota, resulting in the significant changes of gut bacterial genera diversity, metabolic patterns, and fecal metabolite profiles as well as inducing host liver inflammation...
January 17, 2019: Journal of Proteomics
https://read.qxmd.com/read/30659936/lable-free-based-comparative-proteomic-analysis-of-secretory-proteins-of-rough-brucella-mutants
#20
Peng Li, Mingxing Tian, Hai Hu, Yi Yin, Xiang Guan, Chan Ding, Shaohui Wang, Shengqing Yu
Brucella rough mutants are reported to induce infected macrophage death, which is type IV secretion system (T4SS) dependent. T4SS and its secretory proteins play a major role in host-bacteria interactions, but the crucial secretory proteins to promote macrophage death during Brucella rough mutant infection have not been characterized. In this study, we found that T4SS components played no role for macrophage death induced by Brucella rough mutant infection, but some T4SS effectors did. Proteomics of secretory proteins from Brucella rough mutants ΔrfbE and ΔrfbEΔvirB123 was analyzed by liquid chromatography/tandem mass spectrometry and 861 unique proteins were identified, among which 37 were differential secretory proteins...
January 16, 2019: Journal of Proteomics
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