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Proteomics Databases
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• How Does Bottom-Up Proteomics Achieve Precise Quantification?
Bottom-up proteomics, also referred to as analytical proteomics, is a mainstream strategy in proteome research. In this approach, complex protein samples are enzymatically cleaved, most commonly with trypsin, into peptides, which are subsequently identified and quantified using liquid chromatography–tandem mass spectrometry (LC–MS/MS). From these peptide-level data, the composition and abundance of the original proteins are inferred. This method offers high throughput, exceptional sensitivity, and broad....
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Protein purity is a critical parameter influencing both the reliability of downstream experiments and the overall quality of products. High-Performance Liquid Chromatography (HPLC), renowned for its outstanding separation capability and high quantitative accuracy, is widely employed as a key technique for protein purity assessment. This article provides a detailed explanation of the principles, standard operating procedures, and optimization strategies for HPLC-based protein purity analysis. Principles.....
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• How Does LC-MS/MS Advance Bottom-Up Proteomics?
Bottom-up proteomics enables comprehensive protein identification and quantification by enzymatically digesting complex protein samples into peptides, followed by analysis using liquid chromatography–tandem mass spectrometry (LC-MS/MS). This workflow not only enhances the sensitivity and throughput of proteomics research, but also provides a robust methodological foundation for investigating disease mechanisms, discovering biomarkers, and screening drug targets. Basic Principles and Advantages of LC-MS/MS..
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• How to Accurately Identify Membrane Proteins and Low-Abundance Proteins Using Shotgun Proteomics?
Membrane proteins and low-abundance proteins play pivotal roles in biological processes such as cell communication, signal transduction, and molecular transport. Owing to their strong hydrophobicity, low expression levels, and poor stability, they are challenging to identify accurately in conventional proteomic analyses. In recent years, shotgun proteomics, empowered by advancements in mass spectrometry platforms and workflow optimization, has begun to overcome these identification bottlenecks, thereby ....
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• How Does Orbitrap Technology Enable High-Accuracy Sequencing of C-Terminal Peptides?
In proteomics research, precise sequencing of C-terminal peptides is critical for elucidating post-translational modifications, identifying degradation signals, and discovering novel functional peptide segments. The C-terminal region often harbors diverse functional motifs; however, strong structural heterogeneity, weak signal intensity, and enzymatic cleavage constraints have consistently presented significant challenges for mass spectrometric analysis of C-terminal peptides. With the advancement and .....
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• How to Analyze Glycoprotein Modifications with Top-Down Proteomics?
Glycosylation is among the most prevalent post-translational modifications (PTMs), widely occurring in key biological macromolecules such as membrane proteins, secretory proteins, cytokines, and therapeutic antibodies. N-glycosylation and O-glycosylation are integral to protein folding, stability, cell recognition, and signal transduction. Alterations in glycosylation are frequently associated with diverse pathological conditions, including cancer, immune disorders, and neurodegenerative diseases. Owing....
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• How to Improve Quantification Accuracy in Shotgun Proteomics?
Shotgun proteomics is extensively applied in life science research to systematically characterize the protein composition and quantify abundance changes in complex biological samples. Despite its high throughput and broad coverage, quantification accuracy is often compromised by interferences at multiple stages, thereby affecting data reproducibility and the robustness of biological interpretations. This article systematically reviews key strategies for enhancing quantification accuracy in shotgun .........
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• What is Top-Down Proteomics Best Suited For? Applications and Insights
Top-down proteomics (TDP) is an analytical strategy that directly examines intact proteins, in contrast to the bottom-up proteomics approach, which identifies and quantifies proteins through their enzymatic digestion products (typically peptides). By preserving the native state of proteins, the top-down approach enables a more comprehensive characterization of post-translational modifications (PTMs), proteoforms, and related structural information. In recent years, advances in mass spectrometry ......
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• What Is Peptidomics? Overview of Its Workflow and Principles
Proteomics has long been recognized as a pivotal discipline for deciphering cellular functions and elucidating disease mechanisms. In recent years, however, growing attention has been directed toward the degradation products of proteins, endogenous peptides, which harbor valuable physiological and pathological information. Peptidomics has thus emerged as a crucial bridge linking protein expression to functional regulation. What Is Peptidomics? Peptidomics is the systematic investigation of naturally .......
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• What is Shotgun Proteomics? A Complete Guide to Its Principles and Applications
Shotgun proteomics is a high-throughput protein identification strategy based on mass spectrometry, widely applied in comprehensive proteomic analyses of cells, tissues, and complex microbiome samples. Characterized by its untargeted nature, unbiased detection, and deep coverage, it represents one of the mainstream approaches for exploratory proteomic data acquisition in contemporary life science research. This paper systematically examines the fundamental principles, technical workflow, and represent......
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