Resources

Proteomics Databases



Metabolomics Databases

• • How Does Data-Dependent Acquisition Work in LC-MS/MS?

  In proteomics research, LC-MS/MS (liquid chromatography-tandem mass spectrometry) serves as the primary analytical platform, and Data-Dependent Acquisition (DDA) is among the longest-established and most mature data acquisition strategies on this platform. Understanding the detailed workflow of DDA in LC-MS/MS enables researchers to optimize experimental parameters, enhance protein identification depth, and accurately assess data characteristics. Basic Framework of LC-MS/MS Liquid Chromatography (L......

• • What Are the Main Differences Between DDA and DIA MS Methods?

  In LC-MS/MS-based proteomics research, the choice of data acquisition strategy directly determines the depth of protein identification, quantitative accuracy, and inter-batch reproducibility. The two most widely used acquisition modes are DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition). Understanding their underlying principles and scope of application is a critical step in designing an effective experimental workflow. Principles and Characteristics of DDA (Data-Dependent Acqu......

• • 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......