Resources

Proteomics Databases



Metabolomics Databases

• • How to Perform Proteomic Analysis on Paraffin-Embedded Tissue Samples?

  Formalin-fixed paraffin-embedded (FFPE) tissues are widely used in clinical pathology research, encompassing diverse disease types and extensive patient information, and therefore represent valuable resources for proteomics. However, protein crosslinking and chemical modifications introduced during formalin fixation and paraffin embedding pose significant technical challenges for proteomic analysis. Key Challenges in FFPE Sample Proteomic Analysis 1. Protein Crosslinking and Denaturation Formalin fix......

• • How Does Golgi Apparatus Proteomics Reveal Protein Trafficking and Secretion Pathways?

  In eukaryotic cells, the Golgi apparatus functions as a central hub for protein processing and trafficking. It receives newly synthesized proteins from the endoplasmic reticulum, executes post-translational modifications (including glycosylation and phosphorylation), and subsequently directs cargo to destinations such as the plasma membrane, lysosomes, or the extracellular milieu. This highly coordinated transport system is governed by precisely regulated molecular mechanisms, whose elucidation increa......

• • How to Combine DDA and DIA for Deep Proteome Coverage?

  In proteomics research, achieving deeper proteome coverage has consistently been a central objective. With advances in mass spectrometry technologies, Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) have become the dominant strategies, each offering distinct technical strengths. In recent years, hybrid approaches that combine DDA and DIA have increasingly been regarded as effective solutions for improving both identification depth and quantitative accuracy. DDA and DIA: Advant......

• • How to Identify ER Membrane Proteins Using LC-MS/MS?

  The endoplasmic reticulum (ER) is the most extensively distributed and structurally intricate membranous organelle in eukaryotic cells. It plays essential roles in protein synthesis and folding, calcium storage, lipid metabolism, and signal transduction. ER membrane proteins, which are fundamental determinants of ER architecture and function, govern critical processes including the unfolded protein response (UPR), maintenance of calcium homeostasis, and transmembrane trafficking. With the rapid advanc......

• • Quantitative Phosphoproteomics: Comparing SILAC, TMT, and Label-Free Methods

  In phosphoproteomics research, identification of phosphorylation sites alone is insufficient. Quantitative information is the primary driver of biological insight, addressing questions such as which sites undergo significant changes upon stimulation and which signaling pathways are most actively regulated by phosphorylation. These analyses rely critically on accurate and reproducible quantitative strategies. Quantitative phosphoproteomics not only facilitates the discovery of potential biomarkers but ......

• • Normalization and Internal Standards in Quantitative Phosphoproteomics

  In quantitative phosphoproteomics, analyses commonly emphasize differential phosphorylation at specific sites, directional changes (up- or down-regulation), and downstream functional or pathway enrichment. Nevertheless, inappropriate selection of internal references and suboptimal normalization can introduce spurious differences, systematic quantification bias, and, ultimately, misleading biological interpretations. Because phosphopeptides are often low in abundance and exhibit substantial variability......

• • Applications of Phosphoprotein Analysis in Cancer Signaling Research

  Cancer is fundamentally characterized by dysregulation of cellular signaling pathways. Within the highly interconnected landscape of signal transduction, protein phosphorylation serves as a pivotal molecular switch. Precise characterization of phosphorylated proteins enables researchers to better understand how cancer cells evade apoptosis, accelerate proliferation, promote angiogenesis, and even acquire drug resistance. Such studies not only elucidate the molecular basis of cancer initiation and prog......

• • Phosphoproteomics Data Analysis Guide: Commonly Used Software Tools and Workflows

  Protein phosphorylation is among the most prevalent post-translational modifications in eukaryotic cells and regulates a wide range of essential biological processes, including signal transduction, cell-cycle progression, metabolic control, and disease pathogenesis. With advances in high-resolution mass spectrometry, phosphoproteomics has become a key approach for interrogating complex cellular signaling networks. Nevertheless, phosphorylation-centric datasets typically require more stringent quality ......

• • Protein Subcellular Localization

  Protein subcellular localization is not only tightly associated with protein function but also plays a critical role in elucidating disease mechanisms, identifying novel therapeutic targets, and discovering biomarkers. The intracellular microenvironment is highly compartmentalized: mitochondria are responsible for energy metabolism, the nucleus regulates gene expression, and lysosomes mediate macromolecular degradation. Distinct subcellular compartments provide unique biochemical environments, and the......

• • Workflow for High-Throughput PPI Detection via Mass Spectrometry

  Protein-protein interactions (PPIs) are fundamental to cellular processes and underpin virtually all biological activities. Elucidating these interactions not only facilitates a deeper understanding of signaling pathways and physiological functions, but also provides a robust foundation for drug target identification and mechanistic studies of disease. With the rapid advancement of systems biology, there is an increasing demand for high-throughput, quantitative, and systematic approaches to PPI analys......