Resources
Proteomics Databases
Metabolomics Databases
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• The Role of Data-Dependent Acquisition (DDA) in Shotgun Proteomics
In proteomics, shotgun proteomics has become a mainstream approach for global proteome identification by leveraging high-throughput mass spectrometric analysis. Among the available acquisition strategies, data-dependent acquisition (DDA) was one of the earliest and most widely adopted modes and continues to play a central role in novel protein identification and exploratory studies. This article systematically examines the working principles, technical advantages, limitations, and experimental optimiz......
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• Applications of Shotgun Proteomics in Biomarker Discovery
Biomarkers are essential tools for early diagnosis, disease stratification, and personalized therapy. With the rapid advancement of mass spectrometry technologies, proteomics has become an important approach for biomarker discovery. Among the available strategies, shotgun proteomics has demonstrated substantial potential for biomarker screening in complex samples owing to its high throughput, unbiased profiling capability, and broad proteome coverage. Overview of Shotgun Proteomics 1. Technical Princ......
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• How Does Histone Phosphorylation Contribute to DNA Damage Response?
DNA is continuously challenged by endogenous metabolic byproducts and exogenous environmental insults, including ultraviolet light, radiation, and chemical agents. It has been estimated that a mammalian cell may incur tens of thousands of DNA damage events each day. If such lesions are not recognized and repaired promptly, they can lead to genomic instability, impaired cellular function, and even tumorigenesis. To preserve genome integrity, cells have evolved a highly sophisticated DNA damage response......
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• How Does Phosphorylation Interact With Other Histone PTMs?
In epigenetics, histone post-translational modifications (PTMs) are widely recognized as central mechanisms governing chromatin organization and gene expression. Among these modifications, phosphorylation is a highly dynamic and reversible mark that not only plays essential roles in signal transduction and chromatin remodeling, but also engages in extensive crosstalk with other histone PTMs, including acetylation, methylation, and ubiquitination. Together, these modifications help define the intricate......
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• Glycoproteomics in Neuroscience
Glycoproteins are broadly expressed in the nervous system and are involved in critical processes including neuronal development, synapse formation, cell recognition, and signal transduction. Advances in glycoproteomics technologies now allow researchers to systematically profile glycosylation on neuronal surface and secreted proteins. This enables deeper insights into brain functional regulation and reveals the molecular basis of numerous neurological disorders. Functional Roles of Glycoproteins in t......
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• Tools for Glycopeptide Quantitation
Glycosylation, one of the most common and functionally diverse post-translational modifications, plays crucial roles in biological processes such as tumor immunity, infection response, and signal transduction. Glycopeptide quantitation reveals dynamic changes in glycosylation under disease conditions, providing important insights for mechanistic studies and biomarker discovery. However, the complexity, low abundance, and structural heterogeneity of glycopeptides pose significant challenges for data an......
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• Overview of Labeling-Based Strategies for Quantitative Glycoproteomics
Glycoproteins are widely present on the surfaces and in the extracellular environment of mammalian cells, playing central roles in cell recognition, signal transduction, and immune responses. Dynamic glycosylation changes are closely associated with various diseases, particularly tumors, neurodegenerative disorders, and inflammatory responses, where glycoprotein expression and function exhibit substantial heterogeneity. Therefore, high-throughput quantification of the glycoproteome is crucial for gain......
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• Principles and Techniques of Quantitative Glycoproteomics Analysis
Glycosylation is a highly structured and dynamic protein post-translational modification (PTM) widely present in secreted and membrane proteins, involved in numerous biological processes including cell recognition, signal transduction, and immune regulation. Glycoproteomics enables systematic identification and quantification of glycoproteins and their glycosylation sites, revealing functional differences in health and disease, and is increasingly recognized as a critical tool in precision medicine an......
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• Integrated iTRAQ with LC-MS/MS Workflow for Quantitative Proteomics
The advancement of proteomics depends on quantitative strategies that are high-throughput, accurate, and reproducible. Particularly when comparing protein expression across multiple biological states, such as disease models, pharmacological interventions, or developmental stages, stable isotope labeling approaches offer distinct advantages. Among these, the iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-LC-MS/MS-based quantitative workflow is widely adopted in quantitative proteomics owi......
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In modern life sciences research, quantitative proteomics serves as a central tool for elucidating disease mechanisms, identifying biomarkers, and evaluating therapeutic interventions. Among available quantitative strategies, Tandem Mass Tag (TMT) technology is distinguished by its high throughput, multiplexing capability, and quantitative accuracy, and has been widely adopted in both basic research and translational medicine. For many investigators, the major challenges of TMT experiments extend beyo......
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