Resources

Proteomics Databases



Metabolomics Databases

• • Which Biopharmaceuticals Can Be Analyzed by High-Resolution Mass Spectrometry for Molecular Weight?

  High-resolution mass spectrometry (HRMS), owing to its exceptional mass accuracy, high sensitivity, and broad measurable mass range, has become an essential analytical tool in biopharmaceutical research and development. Beyond precise molecular weight determination of complex proteins, HRMS enables the resolution of subtle mass differences, providing critical support for structural characterization, impurity profiling, and quality control of biopharmaceutical products. Below, different categories of b......

• • Acetylated Peptide Enrichment Analysis

  Lysine acetylation is a prevalent post-translational modification (PTM) observed in both eukaryotic and prokaryotic organisms. It participates in epigenetic regulation, cell cycle progression, metabolic pathways, and signal transduction. In particular, histone acetylation plays a critical role in chromatin remodeling and transcriptional regulation, where the acetylation states of histones directly influence gene expression. However, compared with PTMs such as phosphorylation and ubiquitination, system......

• • 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......