Showing papers in "Journal of Proteomics in 2018"

TL;DR: This study proposes for the first time the application of bone proteomics to the estimation of the time elapsed since death and found several new potential biomarkers to address this, demonstrating the applicability of proteomic analyses to forensic sciences.

TL;DR: A genus-wide overview of which available antivenoms may be more efficacious in neutralising human envenomings caused by mambas, irrespective of the species responsible is provided, and major D. polylepis venom components are Kunitz-fold family toxins.

TL;DR: Recent applications of bottom-up proteomics using targeted LC-MS for systems biology research include systems-level investigations focused on posttranslational modifications, protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways.

TL;DR: The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO.

TL;DR: This work developed a systematic strategy that combined multiple enzyme digestion, multidimensional separation for sample preparation and high-resolution tandem MS with Byonic software for intact O-glycopeptide characterization and got the largest data set of site-specific native O- glycoproteome from human serum samples.

TL;DR: Interestingly, 11 virulence factors are found among the MV-associated proteins, including biofilm-promoting proteins and extracellular matrix-binding proteins, which may aid in enterococcal colonization.

TL;DR: This study presents sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins and shows that SWATH MS provides a more reproducible coverage of the matrisome compared to data-dependent analysis (DDA) MS.

TL;DR: This review expounds on avenues through which targeted proteomic methodologies can be constructively implemented in translational research and precision medicine to overcome existing challenges that hinder the success of protein biomarkers in clinics, and to develop precise therapeutics for future applications.

TL;DR: A unique venom proteome of the Pakistani D. russelii from the wild is revealed, in which PLA2 predominated (~60% of total venom proteins), in which the antivenom neutralized the toxicity of the wild Pakistani Russell's viper venom at moderate efficacies.

TL;DR: A rapid, robust and high reproducible DIA-based workflow for streamlined serum proteomic profiling from 1μL serum that doesn't need protein depletion and pre-fractionation, while still being able to detect disease-relevant proteins accurately.

TL;DR: This tutorial provides key statistical concepts that help researchers to design proteomics experiments and shows how to analyze quantitative proteomics data using the recent free and open-source R package MSqRob, which was developed to implement the peptide-level robust ridge regression method for relative protein quantification.

TL;DR: Analysis of individual transcripts and venom protein isoforms produced by specimens of a venomous snake (Bothrops atrox), from the Brazilian Amazon rainforest, revealed that transcriptional and translational mechanisms contribute to venom phenotypic variation.

TL;DR: It is demonstrated that the platelet proteome of patients with early-stage lung or head of pancreas cancer differs considerably compared to that of healthy individuals of matched sex and age and after surgical resection of the tumor.

TL;DR: This review depicts stress response in the sensitive organ of stressed soybean and forms the basis to develop molecular markers related to plant defense under flooding and drought stresses.

TL;DR: This work applied a sequential tissue extraction strategy to describe disease-specific remodeling of human lung tissue in disease, using end-stages of COPD and IPF, and revealed altered solubility of matrisome proteins involved in ECM regulators and cell-ECM communication.

TL;DR: Brain-related, highly specific proteins showed promise as early AD biomarker; protein panel APLP1 and SPP1 had the best diagnostic potential in discriminating MCI from control group, while proteinsAPLP1, SPP 1 and CNTN2 may be indicators of disease progression, demonstrating weak to moderate correlation with cognitive tests.

TL;DR: Three novel serum biomarkers were discovered to reflect the MPY variation of dairy cows, which may be useful in quality control in dairy cow production and for optimizing industrial production of dairy products.

TL;DR: This is the first study to apply SWATH mass spectrometry techniques to characterise proteins contributed by egg yolk based freezing media and to profile cryopreservation induced proteomic changes to ram spermatozoa.

TL;DR: Functional investigations revealed that COM-treated exosomes enhanced IL-8 production from renal tubular cells, activated neutrophil migration, had increased (exosomal) membrane fragility, had greater binding capacity to COM crystals, and subsequently enhanced crystal invasion through extracellular matrix migration chamber.

TL;DR: The transcriptomic and proteomic approach were adopted to characterize the composition of salivary glands and their secreted saliva in three planthoppers, respectively, and gained insight into the interaction between insect and host plant throughSalivary approach, and provided a good resource for functional characterization of effectors.

TL;DR: The potential role of ABA and the proteomic mechanism of its regulation in wound suberization of postharvest kiwifruit was elucidated and GSH-Px, MDHAR, SOD, APX, POD, PAL, CCR, PPO, CYP86B1, DGGT and KCS11 were likely to be the key enzymes that involved the response of A BA to stimulate wound su berization by mediating the antioxidant system, phen

TL;DR: Investigation of pathways involved in intramuscular fat deposition in Longissimus dorsi muscle demonstrated that changes in protein/mRNA levels of sarcomere organization, intracellular signal transduction and regulation of actin cytoskeleton, are involved in IMF deposition.

TL;DR: In this article, a proteomic profile of treated colorectal cancer cells was performed and it was shown that the anti-tumor effects of Citrus-limon nanovesicles is partly mediated by lipid metabolism inhibition, in particular via ACACA downregulation.

TL;DR: This is the first report that the reduced central carbon and energy metabolisms form a characteristic feature as a mechanism of V. alginolyticus in resistance to levofloxacin.

TL;DR: The results shed light on the mechanism of how glucose promoting the amino acids biosynthesis and metabolism to potentiate kanamycin to kill antibiotic-resistant bacteria and suggested that adjusting amino acid biosynthesisand metabolism might be a strategy to become phenotypic resistance to antibiotics in bacteria.

TL;DR: This tutorial used an in-silico approach along with the STRING database and successfully performed a fast simulation of a novel constructed histatin 1 protein-protein network, including both the previously known and the predicted interactors, along with the authors' newly identified interactors.

TL;DR: The results provide the first comparative venomic and anti-venomic analysis of neonate and adult B. irregularis from Guam, further highlighting evolutionary trends in venom composition among rear-fanged venomous snakes.

TL;DR: This review focuses on recent applications of proteomics to the field of cow's milk allergy, from allergens quantification to the diagnosis, treatment and prognosis, and sheds a light on potential future directions and developments.

TL;DR: An overview of the current progress of proteomic research is provided, focusing on discovery and validation of diagnostic biomarkers for CRC, to discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.

TL;DR: 8 different proteins in this subspecies venom were able to be identified for the first time, increasing knowledge about its composition and showing that it is a source of these proteins with possible biotechnological applications.