Resources

Proteomics Databases



Metabolomics Databases

• • How to Perform High-Throughput Shotgun Protein Identification via LC-MS/MS?

  To realize high-throughput shotgun protein identification, liquid chromatography–tandem mass spectrometry (LC–MS/MS) has emerged as one of the most widely adopted and efficient analytical strategies. This technology enables the rapid identification and quantification of thousands of proteins in complex biological samples and is extensively applied in fundamental research, disease mechanism elucidation, and drug target discovery. What Is Shotgun Proteomics? Shotgun proteomics, also referred to as bott......

• • The Impact of LC-MS-Based Quantitative Analysis on Antibody Characterization

  Antibodies are among the most pivotal molecules in contemporary biopharmaceutical research and development. Given their structural complexity and functional diversity, precise characterization is essential in drug development, mechanistic studies, and quality control. Traditionally, antibody analysis has relied on methods such as enzyme-linked immunosorbent assay (ELISA), capillary electrophoresis (CE), and Western blotting. While technically straightforward, these methods present clear limitations in......

• • What Is Shotgun Protein Identification and How Does It Differ from Traditional Methods?

  Shotgun protein identification is a large-scale protein identification strategy that involves enzymatically digesting complex protein mixtures (commonly using trypsin) into peptides, followed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. The resulting spectra are then searched against protein databases to infer the identities of the original proteins. The term shotgun refers to its non-targeted analytical approach; rather than analyzing proteins one by one, it comprehensively ......

• • Strategic Considerations in the Design of ABPP Probes

  Activity-Based Protein Profiling (ABPP) is a functional proteomics approach designed to selectively capture enzymatically active proteins within cells or tissues. Beyond offering protein expression profiles, ABPP provides insight into the actual functional state of enzymes, making it a critical tool for target identification, elucidation of drug mechanisms, and biomarker discovery. Central to the success of ABPP is the rational design of chemical probes. An effective ABPP probe must exhibit high targe......

• • How to Perform High-Throughput Protein Acylation Analysis?

  Protein acylation represents a major class of post-translational modifications (PTMs) that play crucial roles in regulating cellular metabolism, signal transduction, and chromatin remodeling. Recent advances in proteomics, particularly in high-resolution mass spectrometry, have enabled high-throughput profiling of protein acylation. This capability has driven rapid progress in research areas such as metabolic regulation, epigenetics, and biomarker discovery in cancer. What Is Protein Acylation? Prote......

• • A Comprehensive Analysis of Peptide Sequencing Techniques: Advantages, Limitations, and Strategic Selection

  Peptides serve as critical intermediaries linking protein functions to various biological processes. They play increasingly significant roles in biomarker discovery, immunotherapy target identification, and natural product research. Peptide sequencing refers to analytical methods used to determine the amino acid sequence of peptide molecules. Composed of 20 standard amino acids linked via peptide bonds, peptides exhibit diverse biological functions, stability profiles, and binding affinities depending......

• • A Comprehensive Evaluation of ABPP: Advantages, Limitations, and Suitable Research Applications

  Activity-Based Protein Profiling (ABPP), a technology grounded in functional proteomics, enables the detection, enrichment, and identification of catalytically active enzymes within complex biological samples. This review provides an in-depth overview of the underlying principles of ABPP, critically evaluates its methodological strengths and limitations, and outlines representative applications in life sciences. Principles of ABPP Technology ABPP employs activity-based probes (ABPs) to selectively la......

• • Protein Acetylation: Mechanisms and Biological Significance

  Protein acetylation, a critical form of post-translational modification, plays a pivotal role in orchestrating numerous biological processes in eukaryotic cells. In particular, it is centrally involved in chromatin remodeling, metabolic homeostasis, signal transduction, and the regulation of protein stability. Mechanistically, protein acetylation primarily occurs in two distinct forms, N-terminal acetylation and lysine acetylation, each catalyzed by different classes of acetyltransferases. These modif......

• • Beginner’s Guide: How to Start CUT&Tag Analysis

  Cleavage Under Targets and Tagmentation (CUT&Tag) is a chromatin profiling technique that has gained popularity due to its high sensitivity, low background noise, and operational simplicity. However, researchers new to this method may face challenges in getting started. This guide offers a comprehensive introduction for CUT&Tag beginners, covering experimental design, reagent selection, step-by-step protocols, and data analysis to facilitate the successful implementation of CUT&Tag experiments. Defin......

• • A Comprehensive Workflow for Bottom-Up Proteomics Analysis (with Sample Preparation Techniques)

  Bottom-up proteomics is a widely adopted strategy in proteome research, wherein proteins are enzymatically digested into smaller peptide fragments prior to analysis using techniques such as mass spectrometry (MS). By examining these peptides, researchers can infer the composition and properties of the original proteins. This approach, known for its high throughput, sensitivity, and adaptability, is extensively applied in basic biological research, elucidation of disease mechanisms, and drug target dis......