Resources

Proteomics Databases



Metabolomics Databases

• • Label-Free Quantitative Glycoproteomics Using DIA-MS

  Glycoproteins participate extensively in key biological processes such as cell recognition, signal transduction, and immune regulation, and dynamic alterations in their glycosylation states are often closely associated with various diseases. Glycoproteomics has therefore emerged as a crucial approach for biomarker discovery and mechanistic studies. To enable systematic quantification of glycosylated proteins, more stringent analytical requirements have been placed on glycoprotein analysis workflows. D......

• • Comprehensive Workflow for Phosphoproteomics Data Processing and Bioinformatic Interpretation

  Phosphoproteomics, a high-throughput mass spectrometry-based analytical approach for characterizing protein phosphorylation, provides a crucial means to interrogate the regulatory roles of phosphorylation in cellular signaling, cell-cycle control, and metabolic regulation. As a dynamic and reversible post-translational modification (PTM), phosphorylation modulates a broad spectrum of biological processes and has become indispensable in mechanistic studies of signal transduction and disease-relevant pa......

• • Principles and Biological Significance of Protein Lactylation Modification

  Post-translational modification (PTM) is a core regulatory mechanism governing protein function, subcellular localization, and molecular interactions. In addition to classical modifications such as phosphorylation, acetylation, and ubiquitination, an emerging modification - lysine lactylation (Kla) - has been recently uncovered. First reported by Zhang et al. in 2019, lactylation is derived from lactate generated during cellular metabolism, a metabolite traditionally viewed as a terminal product of gl......

• • Protein Quantification Technology‑TMT Labeling Quantitation

  In modern life science research, accurate protein quantification plays a central role in elucidating biological mechanisms, identifying disease biomarkers, and advancing drug development. Compared with label-free quantification approaches, Tandem Mass Tag (TMT)-based quantification has emerged as one of the most widely adopted strategies in proteomics due to its high throughput, multiplexed sample analysis, and reduced inter-batch variability. This article provides a comprehensive overview of TMT labe......

• • Co‑immunoprecipitation (Co‑IP) Overview

  Protein-protein interactions form the molecular basis of cellular signal transduction, metabolic regulation, and disease pathogenesis. As a classical approach for investigating endogenous protein interactions, co-immunoprecipitation (Co-IP) remains widely applied in molecular biology and proteomics research owing to its operational robustness, high specificity, and broad applicability. In particular, Co-IP is well suited for validating interactions between defined protein pairs. What Is Co-immunoprec......

• • What Is the Difference between LFQ and iBAQ?

  In quantitative proteomics, LFQ (Label-Free Quantification) and iBAQ (Intensity-Based Absolute Quantification) represent two widely applied yet conceptually distinct quantification strategies. Although both approaches are derived from DDA (Data-Dependent Acquisition) mass spectrometry data, they differ markedly with respect to quantitative objectives, computational principles, and interpretation of results. A clear understanding of these differences is essential for selecting an appropriate quantifica......

• • Methods for Detecting Protein-Protein Interactions (PPIs)

  Within cells, proteins interact through dynamic and highly complex networks, collectively forming protein-protein interaction (PPI) networks that coordinate signal transduction, metabolism, cell cycle regulation, and disease initiation and progression. Consequently, accurate characterization of protein-protein interactions is essential for understanding biological system functions and underlying pathological mechanisms. What Are Protein-Protein Interactions (PPIs)? Protein-protein interactions (PPIs)......

• • PRM Proteomics Data Processing Workflow

  Parallel reaction monitoring (PRM) is a core targeted proteomics approach characterized by high specificity, high sensitivity, and strong quantitative reproducibility. It has been widely applied to biomarker verification, mechanistic studies, and quantitative analysis of clinical specimens. Importantly, generating high-quality PRM results depends not only on an optimized mass spectrometry platform and experimental workflow, but also on a standardized, rigorous, and well-documented data-processing stra......

• • Efficient Identification of Histone Post-Translational Modifications Using LC-MS/MS

  Histone post-translational modifications (PTMs) constitute a central regulatory mechanism governing chromatin organization and gene expression. Acetylation, methylation, phosphorylation, ubiquitination, and other PTMs collectively form the so-called histone code, which plays a pivotal role in diverse biological processes, including cell differentiation, oncogenesis, and stem cell fate determination. Despite their biological significance, histone PTMs present substantial analytical challenges due to th......

• • Mass Spectrometry-Based Whole Proteome Analysis (Shotgun Proteomics)

  In the era of systems biology, elucidating the physiological states of cells, tissues, and entire organisms can no longer rely exclusively on genomic or transcriptomic information. The proteome, representing the functional molecular layer that directly executes biological processes, has emerged as a critical source of insight into biological systems. Among proteomic methodologies, mass spectrometry-based whole proteome analysis, commonly referred to as Shotgun Proteomics, has become a central analytic......