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21:32 EDT 2nd April 2020 | BioPortfolio

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Showing "ExteNDing proteome coverage with legumain highly specific digestion" PubMed Articles 1–25 of 25,000+

ExteNDing proteome coverage with legumain as highly specific digestion protease.

Bottom-up mass spectrometry-based proteomics utilizes proteolytic enzymes with well character-ized specificities to generate peptides amenable for identification by high throughput tandem mass spectrometry. Trypsin, which cuts specifically after the basic residues lysine and arginine, is the predominant enzyme used for proteome digestion, although proteases with alternative specificity are required to detect sequences that are not accessible after tryptic digest. Here, we show that the hu-man cysteine prote...


Increased Legumain/Smad3 expression in atherosclerotic plaque of rat thoracic aorta.

The purpose of this study was to investigate the role of legumain in the formation and stability of atherosclerotic plaque, as well as to explore the association between legumain with Smad3 pathway in a rat atherosclerosis model.

N-Terminomics/TAILS Profiling of Macrophages after Chemical Inhibition of Legumain.

Legumain (asparaginyl endopeptidase) is the only protease with a preference for cleavage after asparagine residues. Increased legumain activity is a hallmark of inflammation, neurodegenerative diseases, and cancer, and legumain inhibitors have exhibited therapeutic effects in mouse models of these pathologies. Improved knowledge of its substrates and cellular functions is a requisite to further validation of legumain as a drug target. We, therefore, aimed to investigate the effects of legumain inhibition in...


Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases.

Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as ...

Legumain acts on neuroinflammatory to affect CUS-induced cognitive impairment.

Cognitive impairment has been widely recognized as a central feature of depression. Legumain, a lysosomal cysteine protease, plays an important role in cancer, atherosclerosis, inflammation and other pathological conditions. Meanwhile, it has been reported that the activation of legumain aggravates the cognitive impairment in neurodegenerative diseases. In this study, we explored the role of legumain in cognitive impairment of stressed mice. Legumain knockout (legumain KO) and wildtype (WT) mice were divide...

Targeting Proline in (Phospho)Proteomics.

Mass spectrometry-based proteomics experiments typically start with the digestion of proteins using Trypsin, chosen because of its high specificity, availability and ease of use. It has become apparent that the sole use of Trypsin may impose certain limits on our ability to grasp the full proteome, missing out particular sites of post-translational modifications, protein segments or even subsets of proteins. To tackle this problem, alternative proteases have been introduced and shown to lead to an increase ...

A dual workflow to improve the proteomic coverage in plasma using data-independent acquisition-MS.

Plasma is one of the most important and common matrices for clinical chemistry and proteomic analyses. Data-independent acquisition (DIA) mass spectrometry has enabled the simultaneous quantitative analysis of hundreds of proteins in plasma samples in support population and disease studies. Depletion of the highest abundant proteins is a common tool to increase plasma proteome coverage, but this strategy can result in the non-specific depletion of protein subsets with which proteins targeted for depletion i...

Monitoring Universal Health Coverage (UHC) in high Tuberculosis burden countries: Tuberculosis mortality an important tracer of UHC service coverage.

There is a paucity of empiric data evaluating whether Tuberculosis (TB) is a useful surrogate measure for Universal Health Coverage (UHC), despite recognition of the importance of TB control efforts as part of the broader UHC agenda. We hypothesized that indicators of TB burden and coverage are sensitive tracers of UHC, when compared to other disease-specific indicators of service provision.

Improving Proteome Coverage for Small Sample Amounts: An Advanced Method for Proteomics Approaches with Low Bacterial Cell Numbers.

Proteome analyses are often hampered by the low amount of available starting material like a low bacterial cell number obtained from in vivo settings. Here, we adapted the single pot solid-phase enhanced sample preparation (SP3) protocol and combined it with effective cell disruption using detergents for the proteome analysis of bacteria available in limited numbers only. Using this optimized protocol, we could dramatically increase identification of peptides and proteins for different Gram-positive and Gra...

Little Consistency In Evidence Cited By Commercial Plans For Specialty Drug Coverage.

We found wide variation in the evidence that US commercial health plans reported reviewing in their specialty drug coverage policies. There was little consistency in the numbers or types of studies cited by health plans. On average, only 15 percent of health plans' coverage policies cited the same study evaluating a specific drug for a specific indication.

pSILAC method coupled with two complementary digestion approaches reveals PRPF39 as a new E7070-dependent DCAF15 substrate.

Targeting specific ubiquitin E3 ligase for degradation of disease-driven protein has recently been an important concept for cancer therapy, as exemplified by the case of thalidomide for the treatment of multiple myeloma. E7070, an aryl sulfonamide drug, exhibited anticancer activity by targeting the E3 ligase receptor DCAF15, with RBM39 as the only known substrate. Exploration of additional substrates of E7070 would facilitate elucidation of its mechanism of actions. To this end, we used a strategy combing ...

Analysis of the Extracellular Proteome of Colistin-Resistant Korean Strains.

We analyzed the extracellular proteome of colistin-resistant Korean (KAB) strains to identify proteome profiles that can be used to characterize extensively drug-resistant KAB strains. Four colistin-resistant KAB strains with colistin resistance associated with point mutations in and genes were analyzed. Analysis of the extracellular proteome of these strains revealed the presence of 506 induced common proteins, which were hence considered as the core extracellular proteome. Class C ADC-30 and class D OX...

Parallel notched gas-phase enrichment for improved proteome identification and quantitation with fast spectral acquisition rates.

Gas-phase fractionation enables better quantitative accuracy, improves signal-to-noise, and increases sensitivity in proteomic analyses. However, traditional gas-phase enrichment, which relies upon a large continuous bin, results in sub-optimal enrichment as most chromatographic separations are not 100% orthogonal relative to the first MS dimension (MS1 m/z). As such, ions with similar m/z values tend to elute at the same retention time, which prevents the partitioning of narrow precursor m/z distributions ...

Comparing the Association Between Insurance and Mortality in Ovarian, Pancreatic, Lung, Colorectal, Prostate, and Breast Cancers.

Insurance coverage is associated with better cancer outcomes; however, the relative importance of insurance coverage may differ between cancers. This study compared the association between insurance coverage at diagnosis and cancer-specific mortality (CSM; insurance sensitivity) in 6 cancers.

A LysargiNase- and chemical derivatization-based strategy LAACTer facilitating in-depth profiling of C-terminome.

Global identification of protein C-termini is highly challenging due to their low abundance in conventional shotgun proteomics. Several enrichment strategies has been developed to facilitate the detection of C-terminal peptides. One major issue of previous approaches is the limited C-terminome coverage. Herein, we integrated LysargiNase digestion, chemical acetylation on neo-N-terminus, and a-ion-aided peptide matching into polyallylamine-based C-terminomics (termed as LAACTer). In this strategy, we leverag...

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species.

PathDIP was introduced to increase proteome coverage of literature-curated human pathway databases. PathDIP 4 now integrates 24 major databases. To further reduce the number of proteins with no curated pathway annotation, pathDIP integrates pathways with physical protein-protein interactions (PPIs) to predict significant physical associations between proteins and curated pathways. For human, it provides pathway annotations for 5366 pathway orphans. Integrated pathway annotation now includes six model organi...

Microwave and open vessel digestion methods for biochar.

Digestion of biomass derived carbonaceous materials such as biochar (BC) can be challenging due to their high chemical recalcitrance and vast variations in composition. Reports on the development of specific sample digestion methods for such materials remain inadequate and thus require considerable attention. Nine different carbonaceous materials; slow-pyrolyzed tea-waste and king coconut BC produced at 300 °C, 500 °C and 700 °C, sludge waste BC produced at 700 °C, wet fast-pyrolyzed Douglas-Fir...

Dynamic Transcriptome-Proteome Correlation Networks Reveal Human Myeloid Differentiation and Neutrophil-Specific Programming.

Human neutrophilic granulocytes form the largest pool of innate immune cells for host defense against bacterial and fungal pathogens. The dynamic changes that accompany the metamorphosis from a proliferating myeloid progenitor cell in the bone marrow into a mature non-dividing polymorphonuclear blood cell have remained poorly defined. Using mass spectrometry-based quantitative proteomics combined with transcriptomic data, we report on the dynamic changes of five developmental stages in the bone marrow and b...

Differences in peptide generation following in vitro gastrointestinal digestion of yogurt and milk from cow, sheep and goat.

Fermentation of milk is commonly used throughout the world to produce a variety of foods with different health benefits. We hypothesised that due to differences in physicochemical properties and protein sequences among milk from different species and their fermented yogurt samples, their protein digestion and resulting peptide profiles would differ. Cow, goat and sheep milk and yogurt were compared at designated timepoints throughout in vitro gastric and intestinal digestion for differences in peptide profi...

Simulated in vitro infant gastrointestinal digestion of yak milk fat globules: A comparison with cow milk fat globules.

Lipolysis products released during digestion exert positive metabolic impacts on the nutrition of newborns. However, the lipolysis behavior of yak milk lipids during digestion remains unknown. In this study, the simulated in vitro infant gastrointestinal digestion of cow, yak and standardized yak milk fat globules the same size as those from cow milk (Cow MF, Yak MF and Yak SMF) were compared. Although Cow MF showed a higher lipolysis rate at the beginning of gastric digestion, Yak MF and Yak SMF exhibited ...

Specific proteomic adaptation to distinct environments in Vibrio parahaemolyticus includes significant fluctuations in expression of essential proteins.

Bacteria constantly experience changes to their external milieu and need to adapt accordingly to ensure their survival. Certain bacteria adapt by means of cellular differentiation, resulting in the development of a specific cell type that is specialized for life in a distinct environment. Furthermore, to understand how bacteria adapt, it is essential to appreciate the significant changes that occur at the proteomic level. By analyzing the proteome of our model organism V. parahaemolyticus from distinct envi...

Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics.

Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion mea...

Basic Strong Cation Exchange Chromatography, BaSCX, a Highly Efficient Approach for C-Terminomic Studies Using LysargiNase Digestion.

Decoding protein C-termini is a challenging task in protein chemistry using conventional chemical/enzymatic approaches. With the rapid development in modern mass spectrometer, many advanced mass spectrometry (MS) based protein C-termini analysis approaches have been established. Although great progresses have been continually achieved, it is still necessary to develop more efficient approaches in order to discover a proteome-scale protein C-termini (C-terminome), and consequently to help understand their bi...

Site-specific determination of lysine acetylation stoichiometries on the proteome-scale.

Posttranslational modification of proteins (PTMs) offers a versatile mechanism to fine-tune the structure, activity, and interactions of the target proteins. Understanding the dynamics and prevalence of the PTM at the site-specific level will provide mechanistic insight into the physiological significance of the modification pathway in cells and diseases. In this chapter, we describe a highly efficient chemical proteomic workflow for the absolute quantification of lysine acetylation stoichiometry. The strat...

Photo-deposition of Au Nanoclusters for Enhanced Photocatalytic Dye Degradation over TiO Thin Film.

Au nanoparticles (NPs) decorated heterogeneous TiO catalysts are known to be effective in the degradation of various organic pollutants. The photocatalytic performance of such Au-TiO structures remarkably depends on size, morphology and surface coverage of Au NPs decorating TiO. Here we propose an effective way of preparing highly active Au nanoclusters (NCs) decorated TiO thin film by a novel photo-deposition method. By altering the solvent type and as well as the illumination time we achieved well-control...


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