Resources

Proteomics Databases



Metabolomics Databases

• • Advantages and Challenges of PRM in Low-Abundance Protein Quantification

  In proteomics research, accurate low-abundance protein quantification is essential for early biomarker discovery, drug target validation, and the elucidation of complex signaling pathways. However, conventional data-dependent acquisition (DDA) approaches often exhibit limited sensitivity and poor reproducibility when applied to complex biological matrices and extremely low-abundance targets. In recent years, Parallel Reaction Monitoring (PRM) has attracted increasing attention for targeted quantificat......

• • From Sample to Result: A Detailed PRM Quantitative Proteomics Workflow

  In targeted protein quantification research, PRM (Parallel Reaction Monitoring) has been widely applied in biomarker validation, drug development, and mechanistic studies because of its outstanding specificity and sensitivity. However, the effectiveness of PRM depends not only on the performance of the mass spectrometry platform itself, but also on rigorous quality control throughout the entire workflow, from sample preparation to data interpretation. This article outlines the complete PRM quantitativ......

• • What Is Histone 2-Hydroxyisobutyrylation (Khib)?

  Histone 2-hydroxyisobutyrylation (lysine 2-hydroxyisobutyrylation, abbreviated as Khib) is a recently identified type of post-translational modification (PTM) occurring on histone lysine residues. In recent years, it has gradually attracted increasing attention in studies of epigenetics and cellular metabolism. This modification not only contributes to elucidating the regulatory mechanisms of gene expression but also exhibits potential functional roles in various biological processes, including cancer......

• • How Does Histone Phosphorylation Influence Chromatin Structure?

  Histone phosphorylation is an important post-translational modification that plays a critical role in the regulation of chromatin structure, gene expression, and DNA damage responses. By introducing negatively charged phosphate groups, histone phosphorylation alters the electrostatic interactions between histones and DNA. In coordination with other post-translational modifications, it contributes to the formation of the epigenetic “histone code,” thereby influencing whether chromatin adopts an open or......

• • 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......