Resources

Proteomics Databases



Metabolomics Databases

• • 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......

• • What Protein Quantification Strategies Are Used in ER Proteomics?

  The endoplasmic reticulum (Endoplasmic Reticulum, ER) serves as a central hub for intracellular protein production and quality control. Secreted and membrane proteins undergo folding, glycosylation, and assembly in the ER, while this organelle also plays critical roles in lipid biosynthesis and calcium homeostasis. Because ER proteomes are highly enriched in membrane proteins, glycoproteins, and low-abundance regulatory factors, ER proteomics is generally more susceptible to biases introduced during s......

• • How Does Mass Spectrometry Enable Endoplasmic Reticulum Proteome Analysis?

  The endoplasmic reticulum (ER) is the central site for protein folding, N-glycosylation, and secretory pathway regulation. It is also highly enriched with multi-pass transmembrane proteins and complexes associated with membrane contact sites (MCS). Achieving high-quality ER proteome analysis using mass spectrometry requires more than simply running samples on the instrument. Instead, three key aspects must be addressed from the beginning of the workflow: reliable enrichment of ER-derived proteins, mem......

• • What Is Histone Butyrylation (Kbu)?

  With the rapid advancement of epigenetics, histone post-translational modifications (PTMs) have become a central focus for understanding the mechanisms underlying gene expression regulation. From classical modifications such as acetylation (Kac) and methylation (Kme) to more recently identified acylation modifications including crotonylation (Kcr) and butyrylation (Kbu), an increasing number of novel histone acylations have been discovered. Among these, histone butyrylation (Kbu), a lysine acylation m......

• • What Sample Preparation Methods Are Suitable for FFPE Proteomics?

  In clinical research and translational medicine, Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples represent one of the most widely available and longest-preserved types of biological materials. Large FFPE archives have been accumulated in hospitals and pathology departments worldwide, encompassing diverse specimen types such as tumors, inflammatory diseases, and rare disorders. These collections provide unique opportunities for retrospective cohort studies. However, FFPE proteomics is far more c......

• • High-Throughput Immunopeptidomics Profiling For Drug Target Identification

  Target discovery remains a central challenge in modern drug development. This is particularly evident in complex pathological contexts, including cancer, infectious diseases, and autoimmune disorders, where the accurate identification and validation of druggable targets critically determine the success of therapeutic development. In recent years, immunopeptidomics, a mass spectrometry-driven analytical approach, has emerged as a powerful strategy for drug target identification and validation. What Is......

• • End-to-End Immunopeptidomics Services: From Sample to Neoantigen Discovery

  Tumor immunotherapy has undergone rapid advancement in recent years. From immune checkpoint inhibitors to personalized vaccines and TCR-T cell therapies, strategies aimed at precisely activating T cell recognition of tumor cells are increasingly regarded as a central direction in next-generation cancer treatment. Neoantigens, defined as novel peptide sequences arising from tumor-specific genetic mutations, represent ideal targets for eliciting tumor-specific immune responses due to their strong non-se......

• • How Does ABPP Support High-Throughput Compound Screening?

  In the early stages of drug discovery, researchers often need to screen hundreds or even thousands of candidate compounds to identify molecules with favorable potency, selectivity, and safety profiles. Traditional screening approaches, such as enzyme inhibition assays and binding affinity analyses, are amenable to high-throughput implementation, but they generally lack direct functional readouts at the target level. As a result, they cannot provide clear evidence that a compound is exerting its intend......

• • Step-by-Step Protocol for Conducting ABPP Experiments

  Unlike conventional proteomics approaches, ABPP (Activity-Based Protein Profiling) not only identifies protein expression, but also captures protein activity states. It is particularly well suited for functionally important enzyme classes with complex regulatory behavior, such as proteases, phosphatases, and deacylases. How, then, can a complete ABPP experiment be systematically designed and implemented? From probe selection to mass spectrometric analysis, and from sample preparation to data interpret......