Global ETD Search
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Showing 1 to 13 of 13 for “"bottom-up proteomics"”.
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Optimized GeLC-MS/MS for Bottom-Up Proteomics
… and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST …
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Development of ion mobility mass spectrometry deconvolution strategies for use in data-independent acquisition proteomics.
… powers can limit the success of MS-based proteomics approaches. This work highlights the development of IM-MS deconvolution techniques and their utilization with commercial data processing software to improve results from IM-enhanced data-independent acquisition (HDMSᴱ) proteomics …
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Proteomic Evaluation and Cytotoxicity of Red Maple (Acer rubrum) Leaves
… its well-known products include maple syrup and high-quality lumber. The potential medicinal benefits of phenolic compounds extracted from the red maple plant, such as glucitol-core containing gallotannins, include antioxidant, and antiglycation effects as well as their importance in …
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The complexity of bioinformatics: techniques for addressing the combinatorial explosion in proteomics and genomics
… of many hypotheses being considered is best supported by the data at hand. In particular, the field of proteomics often grapples with this challenge, due to being at the confluence of a large number of high-throughput data pipelines. This work presents a series of computational frameworks that …
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Application and Evaluation of a Chemical Modification- and Mass Spectrometry-Based Thermodynamic Assay for the Study of Protein-Ligand Interactions in Complex Mixtures
… change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis …
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Native surface mass spectrometry via static liquid extraction and laser ablation sampling for structural characterization of macromolecules in gas phase.
… aims to combine non-denaturing macromolecular proteomics with structural biology and biophysics to elucidate protein functions. By sampling endogenous proteins from their intact biological matrix, proteins' higher-order structure, reaction stoichiometry, and structural motifs can be evaluated …
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Global and targeted proteomics in Arabidopsis thaliana: A study of secondary metabolism and phytohormone signaling
Proteomics is defined as a tool to explore how proteins control and regulate important molecular and physiological processes. Further, peptide-centric approaches, or bottom-up methods, provide more comprehensive coverage of a proteome compared to whole-protein approaches. This body of work assesses …
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Outlining different perspectives for accurate MS-based proteomics in processed matrices - a case study on European feed control
… silkworm-specific peptides were identified via bottom-up proteomics, antibodies produced and a targeted method with optional IAE developed. Method validation showed a limit of detection (LOD) ≤ 0.05% (w/w) in aquaculture, poultry, and pig feed, with IAE enhancing signal-to-noise at the lowest …
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MS-Based Chemical Proteomics Studies of Extracellular Glycoproteins: Identification, Quantification, and Dynamics
… through mass spectrometry (MS)-based proteomics. First, an enrichment method based on metabolic labeling with a sugar analog, copper-free click chemistry, and MS-based proteomics is employed to target cell-surface glycoproteins from multiple cell lines. The method is universal for all …
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Development and Application of Large-Scale Protein Folding Stability Analysis in Drug Target Identification and Disease Biomarker Discovery
… a novel chemo-selection strategy to improve the bottom-up proteomics readout in proteome-wide limited proteolysis experiments. Another goal of this work is to apply these methods to the target identification of two drugs with known mode of action, and to the biomarker discovery of Parkinson’s …
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Comparative Proteomic Analysis of Neem (Azadirachta indica) Seed and Leaves
… achieved using gel filtration (SEC) on a HiLoad<sup>TM </sup>16/600 Superdex<sup>TM </sup>200 pg column, followed by SDS-PAGE on a 10% Tris/Glycine gel. Proteomic profiles were established by peptide mass fingerprinting using LC-MS/MS. The bioinformatic analysis, using PEAKS Studio 10.5, a …
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Development and application of OmpT-based middle down proteomics
… functioning of a biological system. The goal of proteomics is to provide such information as protein identities, post-translational modifications (PTMs) on proteins, and ultimately, quantification of proteins or their PTM levels from given biological samples, mostly using mass spectrometry. …
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ISG15 conjugation : cellular targets and the lysine selectivity of HERC5
… positive selection. Here, I have used DiGly proteomics, a bottom-up proteomics methodology that employs a general motif antibody to enrich ISGylation site-containing peptides, to characterize HERC5 activities and specificities with respect to residues flanking modified lysines, local …