Resources

Proteomics Databases



Metabolomics Databases

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

  In life science research, epigenetic modifications represent a central focus in the regulation of gene expression. Among these, histone acetylation and butyrylation are two key post-translational modifications (PTMs) that play critical roles in chromatin organization, transcriptional regulation, and disease initiation and progression. Although both modifications occur on lysine residues of histones, they differ significantly in their chemical structures, functional mechanisms, and biological effects. ......

• • What Are the Common Challenges in Histone β-Hydroxybutyrylation Analysis?

  In recent years, histone modifications have been widely recognized as key regulatory mechanisms in the epigenetic control of gene expression. In addition to classical modifications such as acetylation, methylation, and phosphorylation, histone β-hydroxybutyrylation (β-hydroxybutyrylation, Kbhb), as an emerging short-chain fatty acid-derived modification, has attracted increasing attention. β-hydroxybutyrylation not only participates in the regulation of metabolism-related genes but is also closely ass......

• • How to Prepare Samples for Histone β-Hydroxybutyrylation Analysis?

  Histone β-hydroxybutyrylation (β-hydroxybutyrylation, Kbhb) is a recently identified lysine post-translational modification closely associated with cellular metabolic states and has been shown to regulate chromatin structure and gene expression. The abundance of histone β-hydroxybutyrylation is extremely low and frequently coexists with other modifications such as acetylation and methylation, which can easily mask its detection. Therefore, an efficient and highly specific sample preparation workflow i......

• • How Does Formalin Fixation Influence Protein Digestion Efficiency?

  Formalin-fixed paraffin-embedded (FFPE) tissue preservation has long been considered the gold standard for long-term storage of biological specimens and is widely used in pathology and clinical research. However, this preservation strategy also introduces substantial challenges for proteomic analysis, particularly with respect to proteolytic digestion efficiency. Chemical Basis of Formalin Fixation and Its Impact on Protein Structure 1. Mechanism of Formaldehyde Crosslinking The primary active compon......

• • Why Does Cross-Linking Affect FFPE Proteomics and How to Mitigate It?

  In tissue sample preservation, formalin-fixed paraffin-embedded (FFPE) processing is a widely adopted standard approach, particularly in clinical pathology. However, the protein crosslinking induced during FFPE processing poses significant challenges for downstream proteomic analysis. What Is Protein Cross-Linking in FFPE? The core processing steps of FFPE samples include: 1. Tissue fixation using 10% neutral buffered formalin. 2. Dehydration of tissues followed by embedding in paraffin for long-term......

• • How to Perform Mitochondrial Proteomics by LC-MS/MS and What Workflows Are Used?

  Mitochondria are central organelles in cellular energy metabolism. In addition to driving ATP production, they also regulate a variety of biological processes, including apoptosis and redox homeostasis. Comprehensive characterization of the mitochondrial proteome is therefore essential for understanding metabolic disorders, cancer, neurodegenerative diseases, and other mitochondria-associated pathologies. Mass spectrometry-based mitochondrial proteomics has become a key strategy for systematically inv......

• • 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......