Resources

Proteomics Databases



Metabolomics Databases

• • 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......

• • Causes of Co-IP Experimental Failure: Common Pitfalls and Troubleshooting Strategies

  Co-immunoprecipitation (Co-IP) is a classical and widely used technique for investigating protein-protein interactions. Owing to its relatively straightforward workflow, high specificity, and ability to validate interactions under native conditions, Co-IP has been extensively applied in signaling pathway elucidation, protein complex assembly, and mechanistic functional studies. Nevertheless, despite its frequent appearance in the literature, the practical success rate of Co-IP experiments remains a ch......

• • Differences Between Immunoprecipitation and Co-Immunoprecipitation

  In life science research, elucidating how proteins cooperate with one another is fundamental to understanding key biological processes, including signal transduction, transcriptional regulation, and disease mechanisms. Immunoprecipitation (IP) and co-immunoprecipitation (Co-IP) are classical experimental approaches for investigating protein interaction networks and are widely applied in proteomics and cell signaling studies. Despite their similar nomenclature and partially overlapping experimental wor......

• • Overview of Common Analytical Methods in Phosphoproteomics

  Phosphorylation represents one of the most prevalent post-translational modifications, modulating essential cellular processes including signal transduction, cell cycle control, metabolic regulation, and apoptosis. Dysregulated protein phosphorylation is closely associated with multiple diseases, particularly contributing to the pathogenic mechanisms of cancer, diabetes, and neurodegenerative disorders. However, the inherently low abundance, dynamic turnover, and susceptibility to dephosphorylation of......

• • Working Mechanism and Advantages of the iTRAQ Labeling Technique

  High-throughput quantitative analysis across multiple biological samples represents a central objective in proteomics research. With advances in mass spectrometry instrumentation, the iTRAQ labeling technique has gained widespread application in studies of disease mechanisms, drug mechanism-of-action, and biomarker discovery due to its sensitivity, quantitative accuracy, and capacity for multiplexed sample processing. Working Mechanism of the iTRAQ Labeling Technique 1. Principle iTRAQ is an isobaric......

• • Tandem Mass Tag (TMT)-Based Quantitative Proteomics

  In contemporary life sciences, proteomics has emerged as a critical analytical approach for characterizing dynamic biological processes, elucidating disease mechanisms, and identifying drug targets. Tandem Mass Tag (TMT) technology, enabled by high-throughput and multi-sample parallel quantification, has become one of the mainstream strategies for protein quantification. This review summarizes the underlying principles and advantages of TMT labeling, highlights representative applications in proteomic......

• • DIA vs DDA: A Comparative Overview of Data Acquisition Principles in Phosphoproteomics

  Protein phosphorylation is one of the most prevalent and functionally important post-translational modifications (PTMs) involved in cellular signal transduction and regulatory processes. In proteomics research, mass spectrometry (MS) serves as the central analytical tool for the identification of phosphorylation sites. Among available MS data acquisition strategies, data-dependent acquisition (DDA) and data-independent acquisition (DIA) are the two most widely used approaches. These strategies differ ......

• • iTRAQ in Quantitative Proteomics: Principles, Workflow, and Applications

  In comparative proteomic studies involving multi-sample analyses, disease mechanism investigations, and drug target discovery, iTRAQ-based quantitative proteomics has gained widespread adoption due to its high throughput capability, analytical sensitivity, and experimental reproducibility. Principles Underlying iTRAQ-Based Quantitative Proteomics: Achieving Multi-Sample Protein Quantification iTRAQ is an isobaric tagging strategy for peptide-based relative quantification in mass spectrometry. Peptide......

• • Common Challenges in 4D DIA Data Processing and Practical Strategies for Resolution

  With the increasing deployment of four-dimensional proteomics (4D proteomics) in biomarker discovery, drug development, and translational clinical studies, data-independent acquisition (DIA) has become the predominant quantitative acquisition strategy. 4D DIA, enabled by ion mobility (IM) separation, substantially enhances analytical sensitivity and proteome coverage. However, these benefits introduce additional demands for downstream data processing, interpretation, and quality control. The ability t......