Resources

Proteomics Databases



Metabolomics Databases

• • Advantages and Disadvantages of SILAC

  Quantitative analysis of protein expression is a fundamental objective in modern biological research and is widely applied to the elucidation of signal transduction mechanisms, identification of drug targets, and screening of disease biomarkers. With the continued development of mass spectrometry, a variety of quantitative strategies have been introduced. Among them, SILAC (Stable Isotope Labeling by Amino acids in Cell culture) has become one of the mainstream approaches for protein quantification in......

• • How to Identify Lactylation Sites on Histones?

  Histone lactylation, as a newly identified epigenetic modification, has garnered increasing attention. This modification demonstrates that lactate, a metabolic intermediate, is not merely a byproduct of energy metabolism but can also regulate gene expression by modifying lysine residues on histones. Compared with classical modifications such as acetylation and methylation, lactylation establishes a direct link between cellular metabolic states and chromatin dynamics, exhibiting unique biological signi......

• • How Does the ER Proteome Contribute to Secretory Pathway Regulation?

  In eukaryotic cells, the protein secretory pathway is a highly organized transport system that involves multiple organelles, including the endoplasmic reticulum (ER), the Golgi apparatus, vesicles, and the plasma membrane. The ER proteome, serving as the primary entry site of this pathway, is responsible not only for protein synthesis, folding, and initial post-translational modification but also for directly influencing secretion efficiency and protein fate through sophisticated quality control and s......

• • What Is Histone Lactylation and How Is It Analyzed?

  Histone lactylation is the covalent modification of lysine residues on histones by lactate molecules, forming lysine lactylation (Kla). This modification is closely linked to lactate, a product of glycolysis, and represents a novel type of histone modification following acetylation, methylation, and other canonical modifications. As an emerging post-translational modification (PTM), histone lactylation has gained attention in epigenetics and is increasingly recognized for its role in biological proces......

• • How to Perform Histone Lactylation Profiling Using LC-MS/MS?

  Histone lactylation is a post-translational modification in which lactate molecules acylate lysine residues, demonstrating that the glycolytic product lactate can modulate the activation of gene transcription via histone lactylation. As a recently discovered epigenetic modification, histone lactylation has rapidly emerged as a focal point in chromatin biology and metabolic regulation studies. LC-MS/MS (liquid chromatography-tandem mass spectrometry) is a pivotal technique for investigating such post-t......

• • How to Enrich Phosphorylated Histone Peptides for LC-MS/MS?

  In epigenetic research, histone phosphorylation is a critical post-translational modification (PTM) that regulates chromatin structure and gene expression. It plays a pivotal role in processes such as DNA damage repair, cell cycle control, and chromosome condensation, often acting as a molecular signal. However, phosphorylation sites are typically low in abundance, highly dynamic, and histones contain multiple other modifications (e.g., acetylation, methylation, ubiquitination), making efficient and s......

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

  In recent years, advances in metabolomics and epigenetics have increasingly highlighted the direct impact of cellular metabolic states on gene regulation. In this context, histone lactylation, a novel histone post-translational modification, has emerged as a focal point in life science research. This modification demonstrates that lactate is not merely a metabolic byproduct but also functions as a key signaling molecule in epigenetic regulation, thereby providing a new perspective on the interplay bet......

• • From Proteins to Peptides: Complementary Role of Peptidomics and Proteomics

  Proteomics and peptidomics, as closely related yet distinct omics disciplines, represent two complementary approaches to protein-centered research. While proteomics focuses on the identification and quantification of intact proteins, peptidomics emphasizes the in-depth characterization of endogenous peptides. Their complementary integration is increasingly recognized as a critical driver in precision medicine, disease mechanism elucidation, and biomarker discovery. Proteomics 1. From Protein Identifi......

• • The Key Role of Peptidomics in Biomarker Discovery

  With the increasing recognition of disease heterogeneity, it has become evident that biomarkers at the genomic and proteomic levels often exhibit limited sensitivity, particularly in early-stage lesions and dynamically regulated conditions. Peptidomics, an emerging omics discipline focused on endogenous peptides, is increasingly regarded as a functional layer in biomarker research. Owing to its unique biological relevance and compatibility with mass spectrometry-based analysis, peptidomics provides a ......

• • 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......