Resources

Proteomics Databases



Metabolomics Databases

• • Quantitative Analysis of SWATH Proteomics Using OpenSWATH: A Complete Workflow Overview

  SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) is a mass spectrometry technique based on Data-Independent Acquisition (DIA), and has gained widespread adoption in proteomics research in recent years. Owing to its excellent reproducibility, high throughput, and comprehensive proteome coverage, it has become a preferred approach for large-scale quantitative analysis. Among the available tools for processing DIA data, OpenSWATH stands out as one of the most widely used, offering an...

• • SWATH-MS vs DDA-MS: Which Technique Is Suitable for Your Research?

  In proteomics research, selecting an appropriate mass spectrometry acquisition method is crucial for obtaining high-quality data. Among the most prevalent approaches are SWATH-MS (Sequential Window Acquisition of all Theoretical fragment ion spectra) and DDA-MS (Data-Dependent Acquisition), each offering distinct advantages. A clear understanding of their underlying principles, application contexts, and technical limitations can guide researchers in developing sound experimental strategies. What Is DDA.....

• • Applications and Breakthroughs of SWATH Proteomics in Agricultural Research

  In the era of precision and intelligent agriculture, elucidating the molecular mechanisms within crops and related organisms has become central to advancing crop breeding, improving disease management, and enhancing the quality of agricultural products. In recent years, SWATH (Sequential Window Acquisition of All Theoretical Mass Spectra) proteomics, a technique based on the Data-Independent Acquisition (DIA) approach, has emerged as a powerful analytical tool in agricultural research due to its .......

• • SWATH-MS Enables Plant Proteomics Research: From Experiment to Data Analysis

  Plants, as complex and functionally diverse biological systems, display highly dynamic molecular regulatory mechanisms in response to environmental stress and in controlling their growth and development. To gain a deeper understanding of the fundamental processes underlying plant life, proteomics has emerged as a vital research tool, complementing genomics and transcriptomics. With advances in mass spectrometry, SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectra) is .......

• • Label-Free Quantitative Proteomics Service Based on SWATH Technology

  With the advancement of proteomics research, label-free quantification techniques have garnered significant attention in fields such as disease mechanism elucidation, biomarker discovery, and drug development, owing to their high throughput and elimination of complex sample pretreatment. Among these, SWATH (Sequential Windowed Acquisition of All Theoretical Fragment Ion Spectra), a Data-Independent Acquisition (DIA) strategy, has emerged as a core methodology in label-free quantitative proteomics. It.......

• • Applications and Strategies of SWATH-MS-Based Proteomics in Clinical Research

  In contemporary clinical research, elucidating the molecular mechanisms of diseases, identifying early diagnostic biomarkers, and guiding personalized therapeutic strategies are recognized as core scientific challenges. As a pivotal tool linking gene expression to phenotypic variation, proteomics has been extensively employed across disciplines such as oncology, immunology, and neuroscience. In recent years, SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectra), a data.......

• • What Is DIA and SWATH? Understanding Data-Independent Acquisition in Proteomics?

  Mass spectrometry is a core technology in modern proteomics research. The choice of acquisition strategy critically influences data coverage, reproducibility, and quantitative accuracy. In recent years, Data-Independent Acquisition (DIA) has rapidly gained prominence and is increasingly considered a mainstream alternative to Data-Dependent Acquisition (DDA). Within the DIA framework, the most widely recognized implementation is SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ion ........

• • High-throughput SWATH-MS Quantitative Proteomics for Biomarker Discovery

  Biomarkers are essential for early disease screening, subtype classification, personalized therapy, and treatment monitoring. As clinical research becomes increasingly precise, the technical demands for biomarker discovery have risen, particularly in the accurate detection of low-abundance proteins and achieving cross-batch data consistency. Mass spectrometry remains a cornerstone of proteomics research. However, the Data-Dependent Acquisition (DDA) approach, due to its stochastic sampling strategy, is.....

• • Beginner's Guide to SWATH-MS Proteomics: Principles, Advantages, and Applications

  Proteomics has become a central technology in modern life sciences for exploring cellular biology, disease mechanisms, and the discovery of biomarkers. SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra), a prominent technique in data-independent acquisition (DIA) strategies, is increasingly recognized as a new standard in proteomics due to its high throughput, strong reproducibility, and extensive coverage. What Is SWATH-MS? SWATH-MS is a mass spectrometry technique based on the DIA...

• • DIA/SWATH-Based Quantitative PTM Analysis

  Post-translational modifications (PTMs) play a central role in regulating cellular functions, signal transduction, metabolic processes, and the development of diseases. Modifications such as phosphorylation, acetylation, ubiquitination, and methylation confer spatiotemporal specificity and functional diversity to proteins, providing critical insights into their functional states. With advances in mass spectrometry, data-independent acquisition (DIA) techniques—particularly the SWATH-MS (Sequential .......