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Proteomics Databases



Metabolomics Databases

• • Why ABPP Is Regarded as a Powerful Tool in Functional Proteomics: A Comprehensive Overview of Its Principles and Applications

  Uncovering a Fundamental Challenge: Protein Expression ≠ Protein Activity In life science research and drug development, researchers frequently encounter paradoxical observations: 1. An enzyme shows high expression levels in transcriptomic and proteomic data, yet exhibits no detectable activity during functional validation. 2. Drug treatment results in significant biological effects, even though the expression level of the target protein remains unchanged. 3. Dozens or even hundreds of candidate targe......

• • How to Analyze Subcellular Protein Translocation Using LC-MS?

  Cells are highly dynamic and intricately regulated systems rather than static entities. Under diverse physiological and pathological conditions, proteins often redistribute among distinct subcellular compartments, a process known as subcellular protein translocation. This phenomenon not only reflects alterations in protein functional states but also plays a direct role in essential biological processes such as signal transduction, metabolic regulation, cell cycle control, and apoptosis. Conventional a......

• • Comprehensive Guide to Activity-Based Protein Profiling (ABPP): Principles and Applications

  Conventional proteomic strategies such as data-dependent acquisition (DDA) and tandem mass tag (TMT) labeling focus primarily on quantifying protein expression levels, yet they often overlook the actual functional status of proteins. Activity-Based Protein Profiling (ABPP), a function-oriented proteomic technology, offers a novel approach to identifying functionally active proteins through selective labeling using chemical probes. MtoZ Biolabs is a pioneer in integrating ABPP with high-resolution mass......

• • How to Analyze Exosome Purification Quality?

  Exosomes are extracellular vesicles with diameters of approximately 30–150 nm, secreted by a variety of cell types. They play essential roles in intercellular communication and pathological regulation, particularly in research on cancer, neurodegenerative diseases, and immunology. However, extraction approaches such as ultracentrifugation, polymer-based precipitation, and size-exclusion chromatography frequently introduce protein impurities, lipoproteins, or non-exosomal EVs, which can markedly compro......

• • What Is Membrane Protein Identification?

  Membrane protein identification aims to systematically characterize and quantify cell membrane–associated proteins, including their types, expression levels, and functional attributes. Membrane proteins play central roles in cellular communication, signal transduction, molecular transport, and the regulation of pathological processes. Research in this field has directly contributed to advances in drug discovery, disease diagnosis, and target validation. However, due to their unique physicochemical pro......

• • How to Prevent Non-specific Binding in Co-IP Assays?

  Co-immunoprecipitation (Co-IP) is a classical technique widely employed to study protein–protein interactions. However, non-specific binding frequently interferes with the assay, resulting in false-positive signals and compromising the reliability of the data. Achieving highly specific and high-signal-to-noise Co-IP results requires rigorous experimental design, optimized conditions, and strict control of experimental variables. This article systematically describes effective strategies to minimize no......

• • How to Choose the Right Antibody for Co-IP Assays?

  In life sciences research, elucidating protein–protein interactions (PPIs) is crucial for understanding cellular signaling pathways, disease mechanisms, and the identification of potential drug targets. Among the classical approaches for studying PPIs, co-immunoprecipitation (Co-IP) is widely employed owing to its simplicity and strong specificity. However, the success of a Co-IP experiment critically depends on one key factor, the choice of antibody. An appropriate antibody determines not only the en......

• • TMT MS3 and SPS-MS3: How to Mitigate Ratio Compression and Enhance Quantitative Accuracy

  In tandem mass tag (TMT)-based multiplexed proteomics, researchers frequently encounter a critical issue known as ratio compression. During MS1 acquisition, co-elution of homologous peptides from different samples and interference from co-isolated background ions often lead to dilution of reporter ion intensities, thereby underestimating the true abundance differences. To address this challenge, both instrument manufacturers and methodological researchers have developed TMT MS3 and Synchronous Precurs......

• • What Is Olink Proteomics ?

  Proteins are the fundamental effectors of biological processes, playing central roles in activities ranging from signal transduction to metabolic regulation. In basic research, the investigation of disease mechanisms and biomarker discovery, proteomics has become an indispensable and powerful analytical approach. However, mass spectrometry-based proteomics (e.g., DDA/DIA) still faces several challenges, including: (1) Limited Sensitivity: difficulty in detecting low-abundance cytokines or extracellula......

• • What Are the Best Software Tools for Shotgun Proteomics Analysis?

  In shotgun proteomics, the large number of tandem mass spectra (MS/MS) generated by liquid chromatography–tandem mass spectrometry (LC–MS/MS) represent only the raw experimental data. Accurate protein identification, reliable quantification, and in-depth functional annotation and pathway analysis all depend on a scientifically rigorous and well-structured data analysis workflow. To achieve this, researchers rely on a suite of specialized bioinformatics tools and software platforms that span multiple a......