Resources

Proteomics Databases



Metabolomics Databases

• • 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......

• • Top-Down Protein Sequencing: Advantages, Applications, and Challenges

  With the ongoing advancement of proteomics toward higher structural resolution and functional interrogation, the ability to characterize protein structures and post-translational modifications (PTMs) at the intact-protein level has become crucial for elucidating biological functions and disease mechanisms. Top-Down protein sequencing, which directly analyzes intact protein molecules without prior proteolytic digestion, has demonstrated unique advantages across diverse and complex biological systems in......

• • Olink PEA Technology: Principle and Data Analysis Workflow

  In high-plex protein detection, Olink, leveraging its proprietary Proximity Extension Assay (PEA) technology, has become a widely adopted platform for biomarker discovery and population-based cohort studies. The PEA method integrates dual-antibody specific recognition, nucleic acid-based tagging, and highly sensitive signal amplification, enabling high analytical throughput without sacrificing quantitative accuracy. In this report, we provide a systematic overview of the underlying principles of Olink......

• • How Can TurboID-Based Proximity Labeling Enable the Study of Low-Abundance Protein Interactions?

  Low-abundance proteins constitute essential regulators within the cellular protein network, including transcription factors, signaling modulators, and epigenetic regulatory proteins. However, their intrinsically low abundance, spatiotemporally restricted expression, and transient or weak interactions with binding partners make conventional affinity-based approaches such as immunoprecipitation (Co-IP) and pull-down insufficient to recover their genuine interaction networks. The development of proximity......

• • Key Differences Between iTRAQ, TMT, and Label-Free Proteomics

  In modern proteomics research, selecting an appropriate quantification strategy is crucial. With advances in mass spectrometry, iTRAQ (Isobaric Tags for Relative and Absolute Quantitation), TMT (Tandem Mass Tag), and label-free quantification have emerged as three mainstream approaches that are widely applied in studies of disease mechanisms, drug target screening, and clinical biomarker discovery. Although all three approaches rely on high-resolution mass spectrometry platforms, they differ substanti......

• • Tools for PRM Proteomics Data Analysis

  Parallel Reaction Monitoring (PRM) is a targeted protein quantification approach enabled by high-resolution and high-mass-accuracy mass spectrometry platforms. PRM has been extensively applied in cancer biomarker verification, drug target confirmation, and signaling pathway studies. In contrast to Selected Reaction Monitoring (SRM/MRM), PRM utilizes high-resolution instruments such as Orbitrap or Q-TOF systems to acquire full fragment ion spectra, thereby improving analytical selectivity and quantitat......

• • Quantitative Phosphoproteomics with TMT Labeling

  Protein phosphorylation represents one of the most prevalent and functionally important post-translational modifications (PTMs) in eukaryotic cells. It regulates essential biological processes, including cell proliferation, apoptosis, metabolism, and stress responses, and is intimately associated with major human diseases such as cancer, autoimmune disorders, and neurodegenerative diseases. However, phosphorylation events are characterized by dynamic turnover, low abundance, and susceptibility to ion ......