Resources

Proteomics Databases



Metabolomics Databases

• • Why Does Cross-Linking Affect FFPE Proteomics and How to Mitigate It?

  In tissue sample preservation, formalin-fixed paraffin-embedded (FFPE) processing is a widely adopted standard approach, particularly in clinical pathology. However, the protein crosslinking induced during FFPE processing poses significant challenges for downstream proteomic analysis. What Is Protein Cross-Linking in FFPE? The core processing steps of FFPE samples include: 1. Tissue fixation using 10% neutral buffered formalin. 2. Dehydration of tissues followed by embedding in paraffin for long-term......

• • How to Perform Mitochondrial Proteomics by LC-MS/MS and What Workflows Are Used?

  Mitochondria are central organelles in cellular energy metabolism. In addition to driving ATP production, they also regulate a variety of biological processes, including apoptosis and redox homeostasis. Comprehensive characterization of the mitochondrial proteome is therefore essential for understanding metabolic disorders, cancer, neurodegenerative diseases, and other mitochondria-associated pathologies. Mass spectrometry-based mitochondrial proteomics has become a key strategy for systematically inv......

• • From Sample Preparation to Data Analysis: End-to-End Workflow of Shotgun Proteomics

  Shotgun proteomics is currently one of the most widely employed strategies in proteomics research. It enables large-scale protein identification and quantification by enzymatically digesting complex protein mixtures into peptides and integrating liquid chromatography-tandem mass spectrometry (LC-MS/MS). This approach is extensively applied to investigate disease mechanisms, discover biomarkers, and study protein functions. Here, we provide a systematic overview of the complete shotgun proteomics workf......

• • Core Advantages of Mass Spectrometry-Based Shotgun Proteomics

  Shotgun proteomics, also referred to as whole-proteome analysis, is one of the most widely applied strategies in contemporary life sciences research. Utilizing high-resolution mass spectrometry, this approach enables comprehensive identification and quantification of proteins in complex samples without relying on antibodies or pre-defined targets, thereby substantially expanding the scope of proteomics applications. Fundamental Workflow of Shotgun Proteomics Shotgun proteomics follows a digest-then-a......

• • Principles of Mass Spectrometry in Shotgun Proteomics

  Shotgun proteomics is one of the most widely employed strategies in contemporary proteomics research, particularly well-suited for high-throughput protein identification and quantification in complex biological samples. This approach enables comprehensive proteome analysis by enzymatically digesting proteins into peptides, followed by mass spectrometric analysis. With the rapid advancement of mass spectrometry technologies, shotgun proteomics has found broad applications across multiple areas of life ......

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

  With the rapid advancement of epigenetics research, histone post-translational modifications (Histone Post-Translational Modifications, PTMs) have become a central focus for elucidating mechanisms of gene expression regulation. Traditional studies have primarily concentrated on classical histone modifications such as acetylation, methylation, and phosphorylation. In recent years, however, a novel metabolism-associated modification, histone lysine β-hydroxybutyrylation (Histone Lysine β-Hydroxybutyryla......

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

  Histone phosphorylation is a key epigenetic modification involved in the regulation of gene expression. By altering chromatin structure, recruiting regulatory proteins, and interacting with other histone modifications, it regulates a wide range of biological processes, including gene transcription, DNA damage repair, and cell-cycle progression. Basic Concepts of Histone Phosphorylation Histones are positively charged basic proteins around which DNA wraps to form nucleosomes, the fundamental structura......

• • What Are the Key Techniques for Histone Phosphorylation Analysis?

  Histone phosphorylation is an important modification involved in epigenetic regulation and participates in multiple biological processes, including gene transcription, DNA repair, and chromatin remodeling. Because histone phosphorylation is characterized by numerous modification sites, strong dynamic regulation, and low abundance, its analysis requires highly sensitive and precise analytical technologies. Research Challenges of Histone Phosphorylation Before discussing specific technologies, it is im......

• • 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......