Resources

Proteomics Databases



Metabolomics Databases

• • From Sample Preparation to Data Analysis: End-to-End Workflow of Shotgun Proteomics

  Shotgun proteomics is currently one of the most widely employed strategies in proteomics research. It enables large-scale protein identification and quantification by enzymatically digesting complex protein mixtures into peptides and integrating liquid chromatography-tandem mass spectrometry (LC-MS/MS). This approach is extensively applied to investigate disease mechanisms, discover biomarkers, and study protein functions. Here, we provide a systematic overview of the complete shotgun proteomics workf......

• • Core Advantages of Mass Spectrometry-Based Shotgun Proteomics

  Shotgun proteomics, also referred to as whole-proteome analysis, is one of the most widely applied strategies in contemporary life sciences research. Utilizing high-resolution mass spectrometry, this approach enables comprehensive identification and quantification of proteins in complex samples without relying on antibodies or pre-defined targets, thereby substantially expanding the scope of proteomics applications. Fundamental Workflow of Shotgun Proteomics Shotgun proteomics follows a digest-then-a......

• • Principles of Mass Spectrometry in Shotgun Proteomics

  Shotgun proteomics is one of the most widely employed strategies in contemporary proteomics research, particularly well-suited for high-throughput protein identification and quantification in complex biological samples. This approach enables comprehensive proteome analysis by enzymatically digesting proteins into peptides, followed by mass spectrometric analysis. With the rapid advancement of mass spectrometry technologies, shotgun proteomics has found broad applications across multiple areas of life ......

• • What Is the Difference Between Histone Kbhb and Acetylation?

  With the rapid advancement of epigenetics research, histone post-translational modifications (Histone Post-Translational Modifications, PTMs) have become a central focus for elucidating mechanisms of gene expression regulation. Traditional studies have primarily concentrated on classical histone modifications such as acetylation, methylation, and phosphorylation. In recent years, however, a novel metabolism-associated modification, histone lysine β-hydroxybutyrylation (Histone Lysine β-Hydroxybutyryla......

• • What Is the Role of Histone Phosphorylation in Epigenetic Regulation?

  Histone phosphorylation is a key epigenetic modification involved in the regulation of gene expression. By altering chromatin structure, recruiting regulatory proteins, and interacting with other histone modifications, it regulates a wide range of biological processes, including gene transcription, DNA damage repair, and cell-cycle progression. Basic Concepts of Histone Phosphorylation Histones are positively charged basic proteins around which DNA wraps to form nucleosomes, the fundamental structura......

• • What Are the Key Techniques for Histone Phosphorylation Analysis?

  Histone phosphorylation is an important modification involved in epigenetic regulation and participates in multiple biological processes, including gene transcription, DNA repair, and chromatin remodeling. Because histone phosphorylation is characterized by numerous modification sites, strong dynamic regulation, and low abundance, its analysis requires highly sensitive and precise analytical technologies. Research Challenges of Histone Phosphorylation Before discussing specific technologies, it is im......

• • How Does Data-Dependent Acquisition Work in LC-MS/MS?

  In proteomics research, LC-MS/MS (liquid chromatography-tandem mass spectrometry) serves as the primary analytical platform, and Data-Dependent Acquisition (DDA) is among the longest-established and most mature data acquisition strategies on this platform. Understanding the detailed workflow of DDA in LC-MS/MS enables researchers to optimize experimental parameters, enhance protein identification depth, and accurately assess data characteristics. Basic Framework of LC-MS/MS Liquid Chromatography (L......

• • What Are the Main Differences Between DDA and DIA MS Methods?

  In LC-MS/MS-based proteomics research, the choice of data acquisition strategy directly determines the depth of protein identification, quantitative accuracy, and inter-batch reproducibility. The two most widely used acquisition modes are DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition). Understanding their underlying principles and scope of application is a critical step in designing an effective experimental workflow. Principles and Characteristics of DDA (Data-Dependent Acqu......

• • What Is the Role of Butyrate in Histone Butyrylation?

  Over the past decade, advances in high-resolution mass spectrometry have enabled the systematic identification of numerous novel histone post-translational modifications (PTMs). Beyond acetylation, butyrylation has emerged as an important focus in epigenetic research. As a widely available short-chain fatty acid (SCFA), butyrate serves not only as a key gut metabolite but also as a direct substrate and regulatory factor for histone butyrylation. What Is Histone Butyrylation? Histone butyrylation is a......

• • How to Use ER Proteomics for Drug Target Discovery?

  The endoplasmic reticulum (ER), one of the largest membranous organelles in cells, plays critical roles in protein folding, post-translational modification, lipid biosynthesis, and calcium homeostasis. Recent studies indicate that ER homeostasis disruption and aberrant activation of the unfolded protein response are central contributors to a variety of diseases. Consequently, systematic analysis of the ER proteome has emerged as a pivotal approach for drug target identification. Technical Foundations......