Resources

Proteomics Databases



Metabolomics Databases

• • 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......

• • What Is the Differences Between Protein Acetylation and Acylation?

  In cellular processes, protein post-translational modifications (PTMs) represent essential mechanisms for regulating protein function, stability, localization, and molecular interactions. Among them, protein acetylation and acylation are two major types of covalent modifications that attach specific chemical groups to defined amino acid residues, most commonly targeting the ε-amino group of lysine (Lys). Basic Definition: Acetylation as a Subclass of Acylation 1. Protein Acetylation Protein acetylati......

• • Principles of Bottom-Up Proteomics

  Bottom-up proteomics is currently one of the most widely used strategies in proteomic research. Its fundamental principle involves enzymatically digesting proteins into peptides, which are then analyzed using mass spectrometry (MS) to infer the identity and characteristics of the original proteins. The central concept of bottom-up proteomics is to first convert complex protein mixtures into smaller peptide fragments, followed by peptide identification and quantification via MS, thereby enabling the re......