Resources

Proteomics Databases



Metabolomics Databases

• • How Machine Learning Enhances Data Analysis in Subcellular Proteomics?

  In the post-genomic era, subcellular proteomics has emerged as a key approach for elucidating cellular functions, protein localization, and the mechanisms underlying dynamic regulation. By performing quantitative and qualitative analyses of proteins across distinct subcellular compartments (e.g., nucleus, mitochondria, endoplasmic reticulum), researchers can characterize the spatial dimension of protein function. However, subcellular proteomics data are typically high-dimensional, noisy, and heterogen......

• • How Subcellular Proteomics Drives Biopharmaceutical Development and Precision Medicine?

  Investigating proteins at the cellular level has become central to elucidating biological processes; however, conventional proteomics often overlooks the spatial distribution of proteins within cells. Subcellular proteomics is reshaping this paradigm. By resolving the precise localization and dynamic translocation of proteins within organelles, researchers can construct a cellular functional map that supports drug-target discovery, mechanism-of-action studies, and precision medicine. What Is Subcellu......

• • How to Analyze Signaling Pathways Using Co‑IP-Based Methods?

  In life science research, immune signaling pathways constitute essential biological systems that maintain immune homeostasis and enable the host to respond to pathogenic challenges. These pathways comprise sequential events involving receptor recognition, intracellular signal transmission, and activation of effector molecules, and they participate broadly in processes such as inflammation, antiviral defense, and autoimmunity. Elucidating the dynamic interactions among proteins within immune pathways i......

• • How to Reduce High Background Signals in Co‑IP Assays?

  High background signals frequently occur in Co-immunoprecipitation (Co-IP) experiments and often present as nonspecific bands, substantial interference in Western blotting, or poorly resolved target protein signals. These issues compromise data reliability and may obscure genuine protein–protein interaction events. To improve assay specificity and reproducibility, this article provides a systematic analysis of potential causes and corresponding optimization strategies across four dimensions: experimen......

• • How to Successfully Perform Co-IP for Low-Expression Proteins?

  In life sciences, accurate identification of protein-protein interactions is essential for elucidating cellular signaling pathways, disease mechanisms, and discovering therapeutic targets. Co-immunoprecipitation (Co-IP), a well-established technique for capturing protein interactions, is widely used across biological systems. Nevertheless, Co-IP analysis of low-expression proteins is often hindered by insufficient signals and substantial background interference. Enhancing the enrichment and detection ......

• • How to Combine Co‑IP with Mass Spectrometry for Protein Interaction Analysis?

  Protein–protein interactions (PPIs) constitute the fundamental cellular network that orchestrates essential biological processes including signal transduction, metabolic pathways, and transcriptional regulation. To elucidate the biological role of a protein, it is crucial not only to determine its expression level but also to characterize its interaction partners. Co-immunoprecipitation coupled with mass spectrometry (Co-IP-MS) has emerged as a powerful strategy for mapping endogenous interaction netw......

• • Key Challenges in Membrane Proteomics and Corresponding Strategies for Resolution

  Membrane proteomics represents one of the most technically demanding areas within proteomic research. It plays a pivotal role in drug target discovery, elucidation of signaling pathways, and the mechanistic study of diseases. However, due to the inherent physicochemical characteristics of membrane proteins and their complex intracellular distribution, membrane proteomics encounters multiple challenges at both the experimental design and data interpretation levels. Major Challenges in Membrane Proteo......

• • Label-Free Shotgun Proteomics as a Strategy for Global Protein Quantification

  Protein quantification is not only a foundational task in proteomics research but also a key step in elucidating the link between biological phenotypes and molecular mechanisms. With the ongoing advancements in mass spectrometry (MS), label-free shotgun proteomics has emerged as a widely adopted approach for high-throughput protein quantification, owing to its advantages such as the elimination of chemical labeling, simplified sample processing, and suitability for large-scale sample comparisons. Wha......

• • A Comprehensive Overview of Tandem Mass Tag (TMT)-Based Quantitative Proteomics

  Accurate quantification is fundamental to uncovering biological differences in proteomics research. As experimental designs involving multiple samples and time points become increasingly prevalent, traditional label-free approaches have demonstrated limitations in terms of consistency and throughput. Tandem Mass Tag (TMT)-based quantitative proteomics has emerged as a powerful alternative, offering high-throughput capabilities, low variability, and parallel sample analysis. These features make it an i......

• • Optimized Strategies for Processing Membrane Proteins via FASP or In-Gel Digestion

  Due to their intrinsic properties, high hydrophobicity, low solubility, and strong tendency to aggregate, membrane proteins have long posed technical challenges in proteomics. Efficient extraction, enzymatic digestion, and mass spectrometry (MS) analysis of membrane proteins depend heavily on the selection of appropriate sample preparation strategies. Among the commonly adopted digestion methods, Filter-Aided Sample Preparation (FASP) and in-gel digestion are applicable to membrane protein processing ......