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Proteomics Databases



Metabolomics Databases

• • How to Use SILAC-Based Proteomics to Reveal Dynamic Protein Expression Changes?

  Dynamic alterations in protein expression under varying physiological conditions, signal stimulation, or pharmacological intervention provide critical insights into cellular regulatory networks and mechanistic processes. Compared with endpoint-based detection methods, dynamic proteomics emphasizes capturing the temporal progression of changes at multiple time points rather than merely observing the differences in final outcomes. Stable Isotope Labeling by Amino acids in Cell culture (SILAC), as a ......

• • What Is ABPP and Why It Is Transforming Functional Proteomics?

  What Is ABPP? Activity-Based Protein Profiling (ABPP) is a chemical probe–based proteomic strategy specifically designed to detect the catalytically active states of enzymes, rather than merely measuring their expression levels. ABPP employs Activity-Based Probes (ABPs) that selectively and covalently label the catalytic sites of active enzymes, thereby enabling the identification of enzymes with confirmed functional activity in complex biological samples. This technique represents a close integration of...

• • How SILAC Technology Enhances the Accuracy of Protein Expression Analysis?

  Monitoring dynamic changes in protein expression is fundamental to understanding disease mechanisms, identifying drug targets, and advancing cell biology research. However, conventional protein quantification methods, such as dye labeling, Western blotting, or label-free quantification, often suffer from substantial inter-batch variability, limited quantitative precision, and poor reproducibility. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) represents a transformative advance, enabling...

• • How PRM Proteomics Supports Biomarker Validation?

  Biomarkers are essential tools for early disease diagnosis, prognosis assessment, and therapeutic monitoring, and have become a focus of intensive research in biomedicine. However, how can clinically meaningful biomarkers be screened and validated from among tens of thousands of proteins? Parallel Reaction Monitoring (PRM), a highly specific and high-throughput targeted protein quantification technique, has emerged as a pivotal approach for advancing biomarker research from candidate identification to .....

• • 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....

• • How to Determine Protein Purity by HPLC? A Comprehensive Analysis of Principles and Operational Procedures

  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.....

• • 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..

• • 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 ....

• • 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 .....

• • 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....