Resources

Proteomics Databases



Metabolomics Databases

• • What to Consider When Choosing an MS Platform for Membrane Protein Identification?

  Membrane proteins play essential roles in cellular signal transduction, molecular transport, and immune recognition. Nevertheless, their pronounced hydrophobicity, low abundance, and complex structural features have long posed significant challenges for isolation and identification in proteomics research.  However, substantial differences exist among MS platforms with respect to achievable proteome depth, sensitivity, throughput, and reproducibility. Technical Challenges in Membrane Protein Research ......

• • What Are the Quantitative Methods for Proteomics?

  Quantitative proteomics is a central analytical approach for investigating changes in protein expression and the underlying regulatory mechanisms. In recent years, this field has rapidly evolved to encompass a broad range of high-resolution and high-sensitivity strategies. A clear understanding of the available protein quantification methods, their suitable experimental contexts, and appropriate selection criteria is therefore essential. In the following sections, we systematically summarize the major......

• • How to Map Proteins Across Cellular Compartments Using Mass Spectrometry?

  Cells are highly organized systems in which the spatial distribution of proteins is often a key determinant of their biological function. The same protein may perform entirely different roles when localized to mitochondria versus the nucleus. Consequently, systematic mapping of protein distributions across distinct cellular compartments represents a central objective in basic life science research and serves as a critical foundation for elucidating disease mechanisms and identifying therapeutic target......

• • How to Perform Subcellular Fractionation for Proteomics Analysis?

  Subcellular fractionation represents a critical sample preparation step in proteomics research and is particularly well suited for the investigation of organelle-specific proteomes, including those of mitochondria, the endoplasmic reticulum, and the nucleus. This approach enables the systematic exploration of protein spatial localization, functional compartmentalization, and dynamic relocalization within cells. In this article, we provide a comprehensive overview of the fundamental principles, commonl......

• • Why Is Lysine Acylation Considered a Key Post-Translational Modification (PTM)?

  Lysine acylation represents a class of post-translational modifications (PTMs) occurring on lysine residues and encompasses the canonical acetylation as well as multiple newly characterized acylation types (including propionylation, butyrylation, valerylation, malonylation, succinylation, and others). In recent years, the advancement of high-resolution mass spectrometry has enabled broad detection and characterization of these modifications and has established lysine acylation as an important molecula......

• • Advantages and Disadvantages of DIA in Phosphoprotein Quantification

  In the context of post-translational modification (PTM) research, phosphorylation has been a focal topic due to its essential involvement in cellular signaling regulation, cell-cycle control, and other dynamic biological processes. Data-Independent Acquisition (DIA), representing a newer generation of mass spectrometry (MS) data acquisition strategies, is increasingly adopted for quantitative phosphoproteomics because of its high throughput, enhanced reproducibility, and reduced stochastic sampling. W......

• • HLA Peptidomics Analysis

  Human Leukocyte Antigen (HLA) molecules constitute central components of the adaptive immune system. By presenting peptides derived from intra- or extracellular sources to T cells, they determine the specificity and accuracy of immune recognition. Functioning as antigen-presenting platforms, HLA molecules display peptides generated within cells or acquired from the extracellular environment, thereby initiating T cell-mediated immune recognition and responses. Peptidomic approaches coupled with mass sp......

• • Advantages and Disadvantages of Quantitative Subcellular Proteomics

  Quantitative subcellular proteomics is an analytical strategy that employs mass spectrometry-based methods to quantify proteins across distinct subcellular compartments, including the nucleus, mitochondria, endoplasmic reticulum, and plasma membrane. By characterizing the spatial redistribution of proteins, this approach enables the investigation of dynamic changes within the intracellular environment and provides critical insights into cellular functions, signal transduction pathways, and disease mec......

• • Subcellular Proteomics for Accurate Protein Localization and Drug Targeting

  In proteomics research, the mere presence or abundance of protein expression has become a fundamental metric; however, such information alone is insufficient to elucidate the true functional roles of proteins within the cellular context. Subcellular proteomics has therefore emerged as a powerful approach that achieves unprecedented spatial resolution by systematically mapping protein distributions across distinct subcellular compartments. This methodology is increasingly recognized as a critical tool ......

• • What Is Subcellular Proteomics?

  Subcellular proteomics is a major branch of proteomics that focuses on the systematic investigation of protein localization, expression levels, post-translational modifications, and dynamic changes across distinct subcellular compartments, including the nucleus, mitochondria, endoplasmic reticulum, and lysosomes. By enabling detailed proteomic profiling at the subcellular level, this approach introduces a critical spatial dimension for elucidating cellular functions, signal transduction pathways, dise......