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proteomics analysis tools

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https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#1
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28637836/bacterial-cellulose-shifts-transcriptome-and-proteome-of-cultured-endothelial-cells-towards-native-differentiation
#2
Gerhard Feil, Ralf Horres, Julia Schulte, Andreas F Mack, Svenja Petzoldt, Caroline Arnold, Chen Meng, Lukas Jost, Jochen Boxleitner, Nicole Kiessling-Wolf, Ender Serbest, Dominic Helm, Bernhard Kuster, Isabel Hartmann, Thomas Korff, Hannes Hahne
Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation...
June 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28630811/development-of-a-branched-radio-frequency-ion-trap-for-electron-based-dissociation-and-related-applications
#3
Takashi Baba, J Larry Campbell, J C Yves Le Blanc, Paul R S Baker, James W Hager, Bruce A Thomson
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28630587/the-most-common-technologies-and-tools-for-functional-genome-analysis
#4
Evelina Gasperskaja, Vaidutis Kučinskas
Since the sequence of the human genome is complete, the main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a variety of technologies and tools used in functional genome analysis...
2017: Acta medica Lituanica
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#5
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28625714/proteomic-analysis-of-seminal-plasma-from-locally-adapted-curraleiro-p%C3%A3-duro-bulls-bos-taurus-identifying-biomarkers-involved-in-sperm-physiology-in-endangered-animals-for-conservation-of-biodiversity
#6
E B Menezes, R V de Oliveira, M F van Tilburg, E A Barbosa, N V Nascimento, A L M C S Velho, F B Moreno, R A Moreira, A C O Monteiro-Moreira, G M C Carvalho, A F Ramos, E Memili, A A Moura
The present study was aimed at evaluating the seminal plasma proteins and sperm parameters of Curraleiro Pé-Duro bulls. Semen was collected from 10 bulls by electroejaculation, and sperm parameters were evaluated in fresh and frozen-thawed semen. Seminal plasma proteins were analyzed by 2-D SDS-PAGE and mass spectrophotometry. Tools in computational biology were used to generate bioinformatic knowledge and evaluate gene ontology, protein-protein interactions, phylogenetic trees and multiple sequence alignments...
May 29, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/28621158/signaling-pathway-profiling-using-reverse-phase-protein-array-and-its-clinical-applications
#7
Mari Masuda, Tesshi Yamada
Increased accessibility to next-generation sequencing within the last decade has led to a paradigm shift in cancer treatment from one-size-fits-all medicine to precision medicine providing therapeutic strategies tailored to the requirements of individual patients. However, the effect of even the most successful agent yet tested is only transient, and durable efficacy has yet to be achieved. Genome- and transcriptome-based approaches cannot fully predict the diversity of protein expression patterns or post-translational modifications that directly contribute to cancer pathogenesis and physiology...
June 16, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28619171/proteomic-and-bioinformatic-analyses-of-putative-mannheimia-haemolytica-secretome-by-liquid-chromatography-and-tandem-mass-spectrometry
#8
Sahlu Ayalew, Anthony W Confer, Steve D Hartson, Patricia J Canaan, Mark Payton, Brian Couger
Mannheimia haemolytica is a major bacterial contributor to bovine respiratory disease complex that costs the livestock industry a billion dollars a year in USA. Commercial vaccines are only partially efficacious under field conditions. Earlier studies found that outer membrane protein preparations and culture supernatants can induce immune responses that enhance resistance to challenge by M. haemolytica strains. The objective of this study was to characterize secretome of two M. haemolytica stains grown under two different media...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28611393/in-depth-method-assessments-of-differentially-expressed-protein-detection-for-shotgun-proteomics-data-with-missing-values
#9
Jinxia Wang, Liwei Li, Tao Chen, Jie Ma, Yunping Zhu, Jujuan Zhuang, Cheng Chang
Considering as one of the major goals in quantitative proteomics, detection of the differentially expressed proteins (DEPs) plays an important role in biomarker selection and clinical diagnostics. There have been plenty of algorithms and tools focusing on DEP detection in proteomics research. However, due to the different application scopes of these methods, and various kinds of experiment designs, it is not very apparent about the best choice for large-scale proteomics data analyses. Moreover, given the fact that proteomics data usually contain high percentage of missing values (MVs), but few replicates, a systematic evaluation of the DEP detection methods combined with the MV imputation methods is essential and urgent...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606843/the-effect-of-diosmin-on-the-blood-proteome-in-a-rat-model-of-venous-thrombosis
#10
Cuilin Cheng, Hong Zhang, Yongzhi Li, Yingyu Zhou, Weihong Lu, Lei Yao
This study was designed to find the protein changes of venous thrombosis in Wistar rats with and without diosmin treatment by two-dimensional gel electrophoresis (2-DE) and investigate the effect of a crucial protein known as CEP350 on human vascular endothelial cell growth. Diosmin was prepared from G.verum L. by solvent extraction and identified 98% purification by HPLC after chromatographic purification using macroporous absorption resin (AB-8) and polyamide. Wistar rats were divided into three groups respectively control group, model group and prevention group...
June 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28606611/bioinfra-prot-a-comprehensive-proteomics-workflow-including-data-standardization-protein-inference-expression-analysis-and-data-publication
#11
Michael Turewicz, Michael Kohl, Maike Ahrens, Gerhard Mayer, Julian Uszkoreit, Wael Naboulsi, Thilo Bracht, Dominik A Megger, Barbara Sitek, Katrin Marcus, Martin Eisenacher
The analysis of high-throughput mass spectrometry-based proteomics data must address the specific challenges of this technology. To this end, the comprehensive proteomics workflow offered by the de.NBI service center BioInfra.Prot provides indispensable components for the computational and statistical analysis of this kind of data. These components include tools and methods for spectrum identification and protein inference, protein quantification, expression analysis as well as data standardization and data publication...
June 9, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28591853/neisseria-genomics-current-status-and-future-perspectives
#12
Odile B Harrison, Christoph Schoen, Adam C Retchless, Xin Wang, Keith A Jolley, James E Bray, Martin C J Maiden
High-throughput whole genome sequencing has unlocked a multitude of possibilities enabling members of the Neisseria genus to be examined with unprecedented detail, including the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. To maximise the potential benefit of this for public health, it is becoming increasingly important to ensure that this plethora of data are adequately stored, disseminated and made readily accessible. Investigations facilitating cross-species comparisons as well as the analysis of global datasets will allow differences among and within species and across geographic locations and different times to be identified, improving our understanding of the distinct phenotypes observed...
June 7, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28585084/glycomic-and-glycoproteomic-analysis-of-glycoproteins-a-tutorial
#13
Asif Shajahan, Christian Heiss, Mayumi Ishihara, Parastoo Azadi
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses...
June 6, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28584285/oxygen-atoms-are-critical-in-rendering-thp-1-leukaemia-cells-susceptible-to-cold-physical-plasma-induced-apoptosis
#14
Sander Bekeschus, Kristian Wende, Mohamed Mokhtar Hefny, Katrin Rödder, Helena Jablonowski, Anke Schmidt, Thomas von Woedtke, Klaus-Dieter Weltmann, Jan Benedikt
Cold physical plasma has been suggested as a powerful new tool in oncology. However, some cancer cells such as THP-1 leukaemia cells have been shown to be resistant towards plasma-induced cell death, thereby serving as a good model for optimizing plasmas in order to foster pro-apoptotic anticancer effects. A helium/oxygen radio frequency driven atmospheric plasma profoundly induced apoptosis in THP-1 cells whereas helium, humidified helium, and humidified helium/oxygen plasmas were inefficient. Hydrogen peroxide - previously shown as central plasma-derived agent - did not participate in the killing reaction but our results suggest hypochlorous acid to be responsible for the effect observed...
June 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28582591/a-tool-for-integrating-genetic-and-mass-spectrometry-based-peptide-data-proteogenomics-viewer-pv-a-genome-browser-like-tool-which-includes-ms-data-visualization-and-peptide-identification-parameters
#15
REVIEW
José Eduardo Kroll, Vandeclécio Lira da Silva, Sandro José de Souza, Gustavo Antonio de Souza
In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts...
June 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28580701/identification-of-dj-1-as-a-contributor-to-multidrug-resistance-in-human-small-cell-lung-cancer-using-proteomic-analysis
#16
Hongyi Gao, Yuchun Niu, Man Li, Shun Fang, Linlang Guo
Proteomic approaches have been proven to provide an important tool in identifying drug resistance-associated proteins. The aim of this study was to investigate the protein profiling of drug resistance-related proteins in small-cell lung cancer (SCLC) by proteomic analysis. The proteomic profiling was performed by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with MALDI-TOF-TOF of SCLC in the multidrug-resistant cell line H69AR and its parental cell line H69. A total of 11 proteins were identified to be >2-fold up-or downregulated between the two cell lines...
June 5, 2017: International Journal of Experimental Pathology
https://www.readbyqxmd.com/read/28575146/a-comprehensive-evaluation-of-popular-proteomics-software-workflows-for-label-free-proteome-quantification-and-imputation
#17
Tommi Välikangas, Tomi Suomi, Laura L Elo
Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them...
May 31, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28567482/maldi-tof-mass-spectrometry-for-rapid-differentiation-of-tenacibaculum-species-pathogenic-for-fish
#18
Clara Fernández-Álvarez, Yolanda Torres-Corral, Nancy Saltos-Rosero, Ysabel Santos
Tenacibaculosis is a fish disease that limits the culture of a variety of marine fish species of commercial value in the world. The genus Tenacibaculum includes several species, and their discrimination is of clinical interest in order to improve the management of an outbreak of the disease. In this study, a novel proteomic approach based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis was evaluated for the identification and differentiation of Tenacibaculum species...
May 31, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28562641/pgca-an-algorithm-to-link-protein-groups-created-from-ms-ms-data
#19
David Kepplinger, Mandeep Takhar, Mayu Sasaki, Zsuzsanna Hollander, Derek Smith, Bruce McManus, W Robert McMaster, Raymond T Ng, Gabriela V Cohen Freue
The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra...
2017: PloS One
https://www.readbyqxmd.com/read/28555885/serum-extracellular-vesicles-contain-protein-biomarkers-for-primary-sclerosing-cholangitis-and-cholangiocarcinoma
#20
Ander Arbelaiz, Mikel Azkargorta, Marcin Krawczyk, Alvaro Santos-Laso, Ainhoa Lapitz, Maria J Perugorria, Oihane Erice, Esperanza Gonzalez, Raul Jimenez-Agüero, Adelaida Lacasta, Cesar Ibarra, Alberto Sanchez-Campos, Juan P Jimeno, Frank Lammert, Piotr Milkiewicz, Marco Marzioni, Rocio I R Macias, Jose J G Marin, Tushar Patel, Gregory J Gores, Ibon Martinez, Félix Elortza, Juan M Falcon-Perez, Luis Bujanda, Jesus M Banales
Cholangiocarcinoma (CCA) includes a heterogeneous group of biliary cancers with poor prognosis. Several conditions such as primary sclerosing cholangitis (PSC) are risk factors. Non-invasive differential diagnosis between intrahepatic CCA (iCCA) and hepatocellular carcinoma (HCC) is sometimes difficult. Accurate non-invasive biomarkers for PSC, CCA or HCC are not available. In the search of novel biomarkers, serum extracellular vesicles (EV) were isolated from CCA (n=43), PSC (n=30) or HCC (n=29) patients, and healthy individuals (control, n=32), and their protein content was characterized...
May 26, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
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