keyword
MENU ▼
Read by QxMD icon Read
search

proteomics analysis tools

keyword
https://www.readbyqxmd.com/read/28822126/dimethyl-labeling-based-quantification-of-the-lysine-acetylome-and-proteome-of-plants
#1
Ines Lassowskat, Markus Hartl, Fabian Hosp, Paul J Boersema, Matthias Mann, Iris Finkemeier
Photorespiratory enzymes in different cellular compartments have been reported to be posttranslational modified by phosphorylation, disulfide formation, S-nitrosylation, glutathionylation, and lysine acetylation. However, not much is known yet about the function of these modifications to regulate the activities, localizations, or interactions of the proteins in this metabolic pathway. Hence, it will be of great importance to study these modifications and their temporal and conditional occurrence in more detail...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28820289/recent-advances-in-quantitative-and-chemical-proteomics-for-autophagy-studies
#2
Yin-Kwan Wong, Jianbin Zhang, Zi-Chun Hua, Qingsong Lin, Han-Ming Shen, Jigang Wang
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process...
August 18, 2017: Autophagy
https://www.readbyqxmd.com/read/28815751/flow-cytometry-in-spermatology-a-bright-future-ahead
#3
REVIEW
C Ortega-Ferrusola, M C Gil, H Rodríguez-Martínez, L Anel, F J Peña, P Martín-Muñoz
Techniques such as mass spectrometry have led to unprecedented knowledge of the proteins that are present in the spermatozoa of humans and other mammals. However, in spite of their high-throughput and fractioning techniques, most of the techniques in use only offer average values for the entire sperm population. Yet, ejaculate is very heterogeneous, and average values may mask relevant biological information.The application of flow cytometry may overcome this disadvantage, allowing proteomic analysis at the single-cell level...
August 15, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28815030/a-combined-bile-and-urine-proteomic-test-for-cholangiocarcinoma-diagnosis-in-patients-with-biliary-strictures-of-unknown-origin
#4
Torsten Voigtländer, Jochen Metzger, Bastian Schönemeier, Mark Jäger, Harald Mischak, Michael P Manns, Tim O Lankisch
BACKGROUND: Detection of cholangiocarcinoma (CC) remains a diagnostic challenge particularly in patients with primary sclerosing cholangitis (PSC). We recently established diagnostic peptide marker models in bile and urine to detect CC. Our aim was to combine both models to reach a higher diagnostic accuracy of CC diagnosis. METHODS: Bile (BPA) and urine (UPA) proteome analysis by capillary electrophoresis mass spectrometry was performed in a case-control phase II study on 87 patients (36 CC including 13 with CC on top of PSC, 33 PSC and 18 other benign disorders)...
August 2017: United European Gastroenterology Journal
https://www.readbyqxmd.com/read/28813517/prmepred-a-protein-arginine-methylation-prediction-tool
#5
Pawan Kumar, Joseph Joy, Ashutosh Pandey, Dinesh Gupta
Protein methylation is an important Post-Translational Modification (PTMs) of proteins. Arginine methylation carries out and regulates several important biological functions, including gene regulation and signal transduction. Experimental identification of arginine methylation site is a daunting task as it is costly as well as time and labour intensive. Hence reliable prediction tools play an important task in rapid screening and identification of possible methylation sites in proteomes. Our preliminary assessment using the available prediction methods on collected data yielded unimpressive results...
2017: PloS One
https://www.readbyqxmd.com/read/28808136/eplant-visualizing-and-exploring-multiple-levels-of-data-for-hypothesis-generation-in-plant-biology
#6
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence Kelley, Michael Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J Provart
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data, and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis data through a zoomable user interface...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28802824/highly-accurate-prediction-of-protein-self-interactions-by-incorporating-the-average-block-and-pssm-information-into-the-general-pseaac
#7
Jing-Xuan Zhai, Tian-Jie Cao, Ji-Yong An, Yong-Tao Bian
It is a challenging task for fundamental research whether proteins can interact with their partners. Protein self-interaction (SIP) is a special case of PPIs, which plays a key role in the regulation of cellular functions. Due to the limitations of experimental self-interaction identification, it is very important to develop an effective biological tool for predicting SIPs based on protein sequences. In the study, we developed a novel computational method called RVM-AB that combines the Relevance Vector Machine (RVM) model and Average Blocks (AB) for detecting SIPs from protein sequences...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28798504/molecular-aspects-of-wound-healing-and-the-rise-of-venous-leg-ulceration-omics-approaches-to-enhance-knowledge-and-aid-diagnostic-discovery
#8
REVIEW
Daniel A Broszczak, Elizabeth R Sydes, Daniel Wallace, Tony J Parker
Chronic wounds, in particular venous leg ulcers (VLU), represent a substantial burden for economies, healthcare systems and societies worldwide. This burden is exacerbated by the recalcitrant nature of these wounds, despite best practice, evidence-based care, which substantially reduces the quality of life of patients. Furthermore, co-morbidities such as diabetes and cardiovascular disease within ageing populations further contribute to the increasing prevalence in developed countries. This review provides an overview of the literature concerning the cellular and molecular mechanisms of wound healing and aspects where this process fails, resulting in a chronic wound...
February 2017: Clinical Biochemist. Reviews
https://www.readbyqxmd.com/read/28798251/lungmap-the-molecular-atlas-of-lung-development-program
#9
Maryanne E Ardini-Poleske, Robert Fred Clark, Charles Ansong, James P Carson, Richard A Corley, Gail H Deutsch, James S Hagood, Naftali Kaminski, Thomas J Mariani, Steven S Potter, Gloria S Pryhuber, David Warburton, Jeffrey A Whitsett, Scott M Palmer, Namasivayam Ambalavanan, The LungMAP Consortium
The National Heart Lung and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic crosstalk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults...
August 10, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#10
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28783154/informed-proteomics-open-source-software-package-for-top-down-proteomics
#11
Jungkap Park, Paul D Piehowski, Christopher Wilkins, Mowei Zhou, Joshua Mendoza, Grant M Fujimoto, Bryson C Gibbons, Jared B Shaw, Yufeng Shen, Anil K Shukla, Ronald J Moore, Tao Liu, Vladislav A Petyuk, Nikola Tolić, Ljiljana Paša-Tolić, Richard D Smith, Samuel H Payne, Sangtae Kim
Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography-tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed...
August 7, 2017: Nature Methods
https://www.readbyqxmd.com/read/28763045/mzstudio-a-dynamic-digital-canvas-for-user-driven-interrogation-of-mass-spectrometry-data
#12
Scott B Ficarro, William M Alexander, Jarrod A Marto
Although not yet truly 'comprehensive', modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed...
August 1, 2017: Proteomes
https://www.readbyqxmd.com/read/28761071/phosphopredict-a-bioinformatics-tool-for-prediction-of-human-kinase-specific-phosphorylation-substrates-and-sites-by-integrating-heterogeneous-feature-selection
#13
Jiangning Song, Huilin Wang, Jiawei Wang, André Leier, Tatiana Marquez-Lago, Bingjiao Yang, Ziding Zhang, Tatsuya Akutsu, Geoffrey I Webb, Roger J Daly
Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes. In silico methods for phosphorylation site prediction can provide a useful and complementary strategy for complete phosphoproteome annotation. Here, we present a novel bioinformatics tool, PhosphoPredict, that combines protein sequence and functional features to predict kinase-specific substrates and their associated phosphorylation sites for 12 human kinases and kinase families, including ATM, CDKs, GSK-3, MAPKs, PKA, PKB, PKC, and SRC...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28759593/proteogenomic-analysis-of-the-total-and-surface-exposed-proteomes-of-plasmodium-vivax-salivary-gland-sporozoites
#14
Kristian E Swearingen, Scott E Lindner, Erika L Flannery, Ashley M Vaughan, Robert D Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivo Muller, Aaron Jex, Robert L Moritz, Stefan H I Kappe, Jetsumon Sattabongkot, Sebastian A Mikolajczak
Plasmodium falciparum and Plasmodium vivax cause the majority of human malaria cases. Research efforts predominantly focus on P. falciparum because of the clinical severity of infection and associated mortality rates. However, P. vivax malaria affects more people in a wider global range. Furthermore, unlike P. falciparum, P. vivax can persist in the liver as dormant hypnozoites that can be activated weeks to years after primary infection, causing relapse of symptomatic blood stages. This feature makes P. vivax unique and difficult to eliminate with the standard tools of vector control and treatment of symptomatic blood stage infection with antimalarial drugs...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28757466/identification-of-serum-proteome-signature-of-irritable-bowel-syndrome-potential-utility-of-the-tool-for-early-diagnosis-and-patient-s-stratification
#15
Athanasios Tsigaridas, Athanassios K Anagnostopoulos, Aggeliki Papadopoulou, Stamatia Ioakeim, Anna Vaiopoulou, Ioannis S Papanikolaou, Nikos Viazis, George Karamanolis, Gerasimos J Mantzaris, George T Tsangaris, Maria Gazouli
Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder with high incidence, and great heterogeneity of symptoms. Numerous factors are correlated with IBS development; however, the pathophysiology is not yet clear. In addition, there is no appropriate diagnostic tool available. The aim of this study was the identification of protein expression alterations in IBS patients compared to healthy individuals. Serum samples from 30 IBS patients (10 with IBS-Diarrhea, 10 IBS-Constipation and 10 IBS-Mixed) and 10 healthy individuals were subjected to proteomic analysis by 2-dimensional gel electrophoresis...
July 28, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28755912/examination-of-pathways-involved-in-leukemia-inhibitory-factor-lif-induced-cell-growth-arrest-using-label-free-proteomics-approach
#16
Syed Azmal Ali, Gurjeet Kaur, Ashok Kumar Mohanty, Sudarshan Kumar
Leukemia inhibitory factor (LIF) is a multifunctional highly glycosylated protein, synthesized and secreted in various body tissues. Besides the abundance in multiple organs, the molecular mechanism underlying the LIF interactions for cell survival and polarity is poorly understood. In the present study, high-resolution LC-MS/MS based LFQ approach identified 2083 proteins with the overall PSM as 16,032. This proteomics data reviles that LIF promotes the AKT-mTOR signaling pathway. It induces cell growth arrest by an intracellular pathways loop to increase the half-life of the cell...
July 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28755235/electrophoresis-based-proteomics-to-study-development-and-germination-of-date-palm-zygotic-embryos
#17
Besma Sghaier-Hammami, Noureddine Drira, Mouna Bahloul, Jesús V Jorrín-Novo
Proteomics has become an important and powerful tool in plant biology research. To establish a proteomic reference map of date palm zygotic embryos (ZE), we separated and identified proteins from zygotic embryos during different developmental and germination phases using one, two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Proteins are extracted with trichloroacetic acid (TCA)/acetone-phenol and resolved by gel electrophoresis. Gel images are captured and analyzed by appropriate software and statistical packages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28750864/identification-of-a-new-diagnostic-antigen-for-glanders-using-immunoproteome-analysis
#18
Sudhir K Dohre, Aayushi Kamthan, Sandeep Singh, Syed Imteyaz Alam, Subodh Kumar
Glanders is a disease of horses, donkeys and mules. The causative agent Burkholderia mallei, is a biorisk group 3 pathogen and is also a biothreat agent. Simple and rapid diagnostic tool is essential for control of glanders. Using a proteomic approach and immunoblotting with equine sera, we identified 12 protein antigens that may have diagnostic potential. Various immunoreactive proteins e.g. GroEL, translation elongation factor Tu, elongation factor Ts, arginine deiminase, malate dehydrogenase, DNA directed RNA polymerase subunit alpha were identified on 2-dimentional immunoblots...
August 2017: Comparative Immunology, Microbiology and Infectious Diseases
https://www.readbyqxmd.com/read/28741036/network-based-subcellular-proteomics-in-monocyte-membrane-revealed-novel-candidate-genes-involved-in-osteoporosis
#19
Y Zeng, L Zhang, W Zhu, H He, H Sheng, Q Tian, F-Y Deng, L-S Zhang, H-G Hu, H-W Deng
In this study, label-free-based quantitative subcellular proteomics integrated with network analysis highlighted several candidate genes including P4HB, ITGB1, CD36, and ACTN1 that may be involved in osteoporosis. All of them are predicted as significant membrane proteins with high confidence and enriched in bone-related biological process. The results were further verified in transcriptomic and genomic levels. INTRODUCTION: Osteoporosis is a metabolic bone disease mainly characterized by low bone mineral density (BMD)...
July 24, 2017: Osteoporosis International
https://www.readbyqxmd.com/read/28739138/the-in-silico-zebrafish-matrisome-a-new-tool-to-study-extracellular-matrix-gene-and-protein-functions
#20
Pauline Nauroy, Sandrine Hughes, Alexandra Naba, Florence Ruggiero
Extracellular matrix (ECM) proteins are major components of most tissues and organs. In addition to their crucial role in tissue cohesion and biomechanics, they chiefly regulate various important biological processes during embryonic development, tissue homeostasis and repair. In essence, ECM proteins were defined as secreted proteins that localized in the extracellular space. The characterization of the human and mouse matrisomes provided the first definition of ECM actors by comprehensively listing ECM proteins and classified them into categories...
July 21, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
keyword
keyword
78635
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"