Resources

Proteomics Databases



Metabolomics Databases

• • What Is FFPE Sample Proteomics?

  FFPE sample proteomics refers to the application of mass spectrometry and related technologies to analyze formalin-fixed, paraffin-embedded (FFPE) tissues, aiming to systematically identify, quantify, and characterize protein expression patterns. This approach has been widely utilized in clinical research, cancer biomarker discovery, drug target validation, and investigations of disease mechanisms. What Is an FFPE Sample? FFPE represents the most widely used preservation strategy in histopathology: 1......

• • What Post-translational Modifications Occur in Mitochondrial Proteins?

  Mitochondrial protein modifications represent fundamental mechanisms governing mitochondrial function and cellular metabolic homeostasis. With continuous advances in mass spectrometry technologies, numerous post-translational modifications (PTMs) have been identified on mitochondrial proteins. These modifications influence protein stability, enzymatic activity, and molecular interactions, and are strongly associated with a wide range of diseases, including neurodegenerative disorders, cancer, and meta......

• • 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 ......