Resources

Proteomics Databases



Metabolomics Databases

• • Can Histone Lactylation Affect Transcriptional Activation?

  In the life sciences, histone modifications represent key mechanisms governing gene expression. In recent years, lactate has been recognized not only as a metabolic byproduct but also as a signaling molecule that regulates gene expression through histone lactylation on lysine residues. This modification neutralizes the positive charge of histones, promoting a transition of chromatin from a compact to an open state, thereby facilitating transcription factor binding and RNA polymerase II activity. Conse......

• • What Are the Challenges of Proteomics on FFPE Samples?

  Among clinical sample resources, formalin-fixed paraffin-embedded (FFPE, Formalin-Fixed Paraffin-Embedded) tissues, owing to their advantages such as long-term preservation, abundant availability, and broad coverage of pathological types, represent a highly valuable resource for proteomics research. They are particularly valuable in disease biomarker discovery, tissue-specific protein studies, and retrospective cohort analyses. However, FFPE samples also present numerous technical challenges during pr......

• • How to Improve Protein Recovery From FFPE Tissue?

  In modern life science research, formalin-fixed paraffin-embedded (FFPE) tissue samples are widely used because of their suitability for long-term storage and the extensive clinical resources they provide. However, protein extraction from FFPE tissues remains technically challenging, directly affecting the sensitivity and accuracy of downstream proteomic analyses. Challenges in Protein Recovery from FFPE Tissues During FFPE fixation, formaldehyde induces protein cross-linking, thereby stabilizing tis......

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

  In eukaryotic chromatin regulation, histone post-translational modifications (PTMs) play a pivotal role. Histone acetylation (lysine acetylation, Kac) has long been regarded as a classical modification associated with chromatin relaxation and gene activation. In recent years, however, lysine 2-hydroxyisobutyrylation (Khib) has emerged as a newly recognized modification that has attracted increasing attention. Although both modifications occur on lysine residues, they differ substantially in their chem......

• • What Is the Role of β-Hydroxybutyrate in Histone Modification?

  In recent years, metabolites have emerged not only as sources of energy and building blocks but also as direct regulators of gene expression in biological research. Notably, β-hydroxybutyrate (BHB), an important ketone body, has attracted significant attention for its roles in energy metabolism, neuroprotection, and anti-inflammatory processes. Increasing evidence suggests that BHB can directly modulate gene expression patterns through histone modifications, providing new insights into the metabolism-......

• • What Is the Workflow of Histone Phospho-Proteomics?

  Histone phosphorylation is a critical epigenetic modification that is extensively involved in chromatin remodeling, gene transcription, DNA damage response, and other biological processes. Leveraging high-resolution mass spectrometry, researchers can systematically characterize the dynamic changes of histone phosphorylation sites and elucidate their regulatory roles in cell cycle progression, tumorigenesis, and immune responses. As a key branch of histone modification omics, histone phosphorylation ha......

• • 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......