Resources

Proteomics Databases



Metabolomics Databases

• • 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......

• • How Label-Free Quantification Facilitates Precise Profiling of Lactylated Proteins

  In recent years, lactylation has emerged as a novel post-translational modification (PTM) with crucial roles in biological processes such as metabolic regulation, inflammatory response, and tumorigenesis. However, due to its low abundance, diverse modification sites, and the absence of highly specific antibodies, research on lactylated proteins faces considerable technical challenges. To enable accurate detection and quantification of these proteins, label-free quantification (LFQ) has become a prefer......

• • Principles of PRM Quantitative Proteomics

  Parallel Reaction Monitoring (PRM) is a targeted quantitative proteomic approach that employs high-resolution mass spectrometry. It has become an essential tool for advanced quantitative analysis in life sciences. Compared with the conventional Selected Reaction Monitoring (SRM) technique, PRM utilizes Orbitrap or Time-of-Flight (TOF) mass spectrometers to perform comprehensive monitoring of fragment ions, thereby achieving superior selectivity, sensitivity, and reproducibility. Working Principles o......

• • Unveiling the Mechanisms of Protein Lactylation: From Metabolic Origin to Functional Implications

  In recent years, lysine lactylation (Kla) has emerged as a novel post-translational modification (PTM) with increasing relevance in epigenetic regulation and cellular metabolism, gaining attention as a promising frontier in the post-genomic era. The identification of protein lactylation has significantly broadened our understanding of the interplay between metabolic flux and transcriptional regulation, offering new perspectives for investigating cancer, immune responses, and metabolic disorders. This ......

• • SILAC-Based Strategies for Differential Protein Screening

  Variations in protein expression levels serve as crucial indicators for elucidating biological processes, disease mechanisms, and pharmacological effects. However, due to the intrinsic complexity of proteins and their broad dynamic expression range, achieving accurate and reproducible protein quantification remains a technical challenge in proteomics. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) has emerged to address this issue. SILAC-based differential protein screening incorporate......