Resources

Proteomics Databases



Metabolomics Databases

• • How to Perform Protein Identification Using Tandem Mass Spectrometry (MS/MS)

  With the advancement of high-throughput omics technologies, proteomics has become increasingly central to life science research, disease mechanism investigation, and novel drug target discovery. Unlike the genome, which provides largely static information, the proteome more accurately captures the dynamic states of cells and their physiological functions. Among the diverse analytical strategies in proteomics, tandem mass spectrometry (Tandem Mass Spectrometry, MS/MS) represents the core technology ena......

• • What Is Peptide Mass Fingerprinting (PMF) in Proteomics?

  In proteomics research, the rapid and accurate identification of proteins has long been a central objective of experimental design. Although high-throughput approaches such as tandem mass spectrometry (MS/MS) and data-independent acquisition (DIA) have become dominant in recent years, peptide mass fingerprinting (PMF) remains a classical and efficient protein identification strategy that continues to play an important role in specific analytical contexts. What Is Peptide Mass Fingerprinting (PMF)? P......

• • What Is MS-Based Protein Identification and How Does It Work?

  In modern life science research, protein identification represents a foundational step for elucidating cellular functions, disease mechanisms, and biomarker discovery. With the rapid advancement of proteomics, mass spectrometry (MS)-based protein identification has emerged as a central analytical strategy owing to its high sensitivity, high throughput, and robust quantitative capability. What Is MS-Based Protein Identification? Protein identification refers to the experimental determination of the pr......

• • Label-Free Quantification: Advantages, Applications, and Tools

  In proteomics research, quantitative analysis represents a critical component for elucidating dynamic changes within biological systems. With the rapid advancement of mass spectrometry technologies, label-free quantification (LFQ) has emerged as an important strategy for protein quantification, owing to its streamlined experimental workflow and broad applicability across diverse sample types. What Is Label-Free Quantification (LFQ)? Label-free quantification is a mass spectrometry-based strategy that......

• • ELISA vs LC-MS: Comparing Two Core Methods for Host Cell Protein Detection

  During biopharmaceutical development and manufacturing, monitoring residual host cell proteins (HCPs) is critical for ensuring product safety and therapeutic efficacy. HCPs represent process-related impurities originating from production cell substrates (e.g., Escherichia coli, yeast, or CHO cells). If present in the final formulation, these impurities may elicit immunogenic responses, compromise drug stability, or reduce clinical performance. Within current quality control frameworks, enzyme-linked i......

• • Comprehensive Overview of Immunopeptidomics: From Sample Preparation to Bioinformatic Analysis

  Immunopeptidomics has rapidly emerged as an advanced analytical field focused on identifying and characterizing peptides presented by major histocompatibility complex (MHC) molecules. This approach holds significant promise in tumor immunotherapy, vaccine development, and autoimmune disease research. What Is Immunopeptidomics and Why Is It Important? Immunopeptidomics refers to a mass spectrometry-based omics strategy for profiling peptides (i.e., immunopeptides) presented on MHC molecules. These pe......

• • Challenges and Opportunities of Bottom-Up Proteomics in Single-Cell Proteomics

  Bottom-up proteomics (also known as shotgun proteomics) involves enzymatically digesting proteins into peptides in vitro, identifying the resulting peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and reconstructing the parent proteins based on peptide-level evidence. In contrast to top-down proteomics, which directly analyzes intact protein species, the bottom-up strategy offers superior scalability for high-throughput protein identification but inherently provides fragment-l......

• • Top-Down Proteomics: Strengths, Limitations, and Analytical Implications

  As proteomics continues to progress toward higher resolution and more refined structural characterization, Top-Down Proteomics (TDP), which enables direct mass spectrometric analysis of intact proteins, has emerged as an essential approach for investigating proteoforms, post-translational modifications (PTMs), and functional heterogeneity. Despite its unique analytical advantages over conventional Bottom-Up workflows, Top-Down Proteomics still encounters considerable technical and application constrai......

• • Targeted vs Untargeted Metabolomics Approaches

  Metabolomics is a core discipline within systems biology, focusing on the comprehensive characterization of small-molecule metabolite dynamics in biological systems. With the rapid advancement of mass spectrometry technologies and computational data analysis tools, targeted metabolomics and untargeted metabolomics have emerged as two principal analytical strategies widely applied in disease mechanism studies, drug development, nutritional research, and environmental toxicology. Targeted vs Untargeted......

• • Advantages and Disadvantages of Untargeted Metabolomics

  In life science research, metabolomics serves as a critical bridge between genotype and phenotype. As the final downstream products of biological processes, metabolites most directly reflect the integrated responses of cells, tissues, or whole organisms to genetic regulation, environmental stimuli, and disease states. Among current analytical strategies, untargeted metabolomics, characterized by broad analytical coverage and a high potential for novel discovery, has been widely applied in disease mech......