Showing papers in "Journal of Proteomics in 2015"

TL;DR: ProLuCID was able to identify as many as 25% more proteins than SEQUEST and is able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data.

TL;DR: This manuscript describes the application of BioID, a proximity biotinylation approach, to chromatin-associated proteins, namely core histones and members of the mediator complex, and shows that the approaches were complementary, allowing for purification of different interaction partners.

TL;DR: An optimized method for quantification of HDL proteome is developed, using PRM in concert with a single labeled protein as internal standard, using HDL's most abundant protein apolipoprotein A-I as the internal standard.

TL;DR: The known interactions of tick saliva with the vertebrate immune system are overviewed to serve as a reference for functional characterization of the numerous genes and proteins expressed in tick salivary glands with an ultimate goal to develop novel vector and pathogen control strategies.

TL;DR: Despite the proteomic variations, the use of Thai monovalent and polyvalent antivenoms for N. kaouthia envenomation in the three regions is appropriate as the different venoms were neutralized by the antivenom albeit at different degrees of effectiveness, supporting their uses in theThree populations.

TL;DR: This work describes a software package, mapDIA, for statistical analysis of differential protein expression using DIA fragment-level intensities, and shows that mapDia detects differentially expressed proteins with accurate control of the false discovery rates.

TL;DR: In this article, a catalogue of 1344 experimentally confirmed RNA binding proteins (RBPs) was constructed and the domain architecture of RBPs enabled them to classify them into three groups: classical (29%), non-classical (19%) and unclassified (52%).

TL;DR: It is demonstrated that BioID can be utilized to identify bona fide interacting partners for a chromatin-associated protein in vivo, which will allow for a much improved understanding of protein-protein interactions in a previously inaccessible biological setting.

TL;DR: It was shown that a majority of the kefir peptides were not endogenously present in the raw material milk, but were released from milk caseins by proteases of the microbiota and are therefore specific for the product.

TL;DR: A combined physiological, histological, proteomics and molecular analysis revealed several important pathways associated with chlorophyll deficiency and these findings may be applied to genetic engineering for high photosynthetic efficiency in crops.

TL;DR: The present study reports the first proteomic analysis of the black mamba venom, which revealed a complex venom constituted predominantly by proteins belonging to the Kunitz-type proteinase inhibitor family, which comprises the dendrotoxins, and to α-neurotoxins of the three-finger toxin family.

TL;DR: Physiological measurements suggested that the SE genotype was more efficient in water absorption and could preserve more water presumably by controlling stomata closure and proteins related to oxidative stress, protein processing and photosynthesis showed decreased abundance to a greater extent in the sensitive genotype (SW).

TL;DR: A peptidomic approach for the identification of ACE-inhibitory and antioxidant peptides generated from thornback ray gelatin (Raja clavata) hydrolysates from Bacillus subtilis A26 and Bacillus amyloliquefaciens Neutrase® enzymes is described to expose the potential of thorn back ray gelatin hydrolysate as a source of bioactive peptides.

TL;DR: A surprisingly wide dynamic range and geographical variation of three-finger toxins in cobra venomics is demonstrated, providing a reasonable explanation for the variable neutralization effects of antivenom treatment on victims suffering from cobra snakebite and suggests a simple and economic method to produce potent antivenome with better efficacy.

TL;DR: The results suggest that the AgNPs treated soybeans might have experienced less oxygen-deprivation stress, which might be the key factor for better growth performance of AgNPS treated soybean under flooding stress.

TL;DR: The first comprehensive view of the skin mucosal proteome of S. aurata is obtained and it is revealed that genera belonging to the Lactobacillales order constitute the most abundant microorganism populations in this habitat.

TL;DR: Proteomic is a "phenomic molecular tool" that may help to discriminate avian males on their reproductive capacity and proposed the first evidence of biomarkers related to fertility.

TL;DR: This work has been designed to supply methodological data mining guidelines, describing systematically the steps to be followed in metabolomics data exploration, using a study of aging in a healthy population to represent this data mining process.

TL;DR: Correlation networks reveal robust correlations, i.e. present for at least two breeds, between potential meat tenderness biomarkers and describe biochemical mechanisms underlying muscle to meat conversion.

TL;DR: The protein profile of PMPs obtained by performing four different activation protocols using mass spectrometry-based quantitative proteomics is investigated to suggest a biological link between agonist strength and proteins associated to platelet mediated processes such as activation and degranulation.

TL;DR: This paper presents SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers, and is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium.

TL;DR: The proteome correlates with the functional and toxinological characterizations of the venom, and reflects the pathophysiological effects of envenomation by the Sri Lankan Russell's viper.

TL;DR: Results suggest that S-adenosylmethionine synthetase is involved in the regulation of stress response because it was changed in response to flooding and drought stresses.

TL;DR: Qualitative and quantitative proteomics of the uterine fluid constituents, coupled with bioinformatic analysis, are used to predict the functional role of proteins secreted at each of the three main stages of shell calcification to determine the importance of particular proteins relative to eggshell mineralization.

TL;DR: Evidence is provided that the protein corona that forms around liposomes is strongly affected by the physiological environment, i.e., the serum type, which suggests that the translational of novel pharmaceutical formulations from animal models to the clinic must be evaluated on a case-by-case basis.

TL;DR: Three complementary proteomic methods are used to identify surface proteins involved in adhesion and immunostimulation by P. freudenreichii, which opens new perspectives for its utilization in new functional fermented food products, in clinical trials, and in understanding modulation of gut inflammation by products containing propionibacteria.

TL;DR: In this paper, the shell of a marine mussel, Mytilus coruscus, was analyzed and three shell layers with different morphologies and polymorphs were observed, which includes nacre, fibrous prism, and myostracum strongly attached by adductor muscles to the interior of the shell surface.

TL;DR: The results indicate that during chronic exposure to sub-lethal concentrations of Cu(2+), the cells tune down their metabolic rate to invest energy in the activation of detoxification mechanisms, which eventually result in a remarkable recovery, in contrast, the toxic effects of Cd(2+) are cumulative.

TL;DR: This study provides the first identification of immune markers through an analysis of the differential expression of both genes and their corresponding protein products in the spleen of rainbow trout after infection by A. salmonicida, shedding light on the molecular mechanisms triggered in rainbow trout against A. Salmonicida and providing new molecular targets for further immunological research in fish.

TL;DR: It is demonstrated that sputum profiling can capture the complex and reversible physiological response to cigarette smoke exposure, which appears to be only slightly modulated in early-stage COPD.