Resources

Proteomics Databases



Metabolomics Databases

• • From TMT to SWATH: Evolution of Quantitative Proteomics Technologies

  In proteomics research, quantitative analysis of proteins plays a pivotal role in elucidating cellular states, understanding disease mechanisms, and identifying potential biomarkers. With the rapid advancement of mass spectrometry (MS) technologies, protein quantification approaches have evolved significantly—from early 2D gel-based techniques to modern high-throughput platforms such as Tandem Mass Tag (TMT) and Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH). This review outlines ....

• • How 4D-DIA Enhances Protein Identification in Complex Samples?

  In proteomics research, sample complexity is a critical factor influencing data quality. Biological specimens such as tissue, body fluids, and archived clinical materials typically exhibit a wide diversity of proteins, a broad dynamic range of abundance, and the presence of numerous interfering substances—factors that pose significant challenges for protein identification and quantification. Although Data-Independent Acquisition (DIA) technology offers high reproducibility and throughput, it often suffers..

• • GPF-DIA vs Direct DIA: Which is Better for Large-Scale Protein Quantification?

  In large-scale proteomics research, Data-Independent Acquisition (DIA) has become a mainstream approach due to its high throughput, excellent reproducibility, and comprehensive data coverage. The advancement of DIA has fostered the development of multiple strategies, with GPF-DIA (Gas Phase Fractionation DIA) and Direct DIA being the most prevalent. These two methods differ significantly in spectral library construction, experimental workflow, and application scenarios. This article presents a systematic...

• • DIA Proteomics Services for Cancer Biomarker Discovery

  Cancer is a highly heterogeneous and complex disease, characterized by diverse molecular mechanisms and intricate biological pathways underlying its initiation and progression. Despite continued advancements in therapeutic strategies, early diagnosis remains a critical determinant for improving cancer prognosis. The discovery and validation of biomarkers represent a pivotal approach for enabling early detection, disease surveillance, and therapeutic response prediction. Among the various omics .......

• • Typical Applications of DIA-Based Quantitative Proteomics in Clinical Research

  In the post-genomic era, proteomics has emerged as a powerful approach for elucidating disease mechanisms, identifying biomarkers, and informing therapeutic decisions. Mass spectrometry (MS), with its high throughput, label-free capabilities, and broad dynamic range, holds significant promise in clinical research. Among various MS acquisition methods, Data-Independent Acquisition (DIA) has become a central technology in clinical proteomics, owing to its superior data reproducibility and comprehensive ......

• • DIA vs DDA Proteomics: Key Differences and Applications Explained

  In proteomics research, mass spectrometry serves as a central technique for elucidating cellular protein composition, changes in protein abundance, and post-translational modifications. Notably, liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analytical approaches have been extensively employed across a range of domains, including basic research, clinical studies, and biomarker discovery. Among various acquisition strategies, Data-Dependent Acquisition (DDA) and Data-Independent .......

• • Principles and Workflow of DIA Proteomics: A Case Study of SWATH-MS

  In the post-genomic era, researchers have increasingly turned their attention to dynamic changes at the proteomic level, aiming to address the limitations of genomic and transcriptomic data. Mass spectrometry (MS), as a central tool in modern proteomics, continues to expand both the depth and breadth of biomedical research. Among the various acquisition strategies, Data-Independent Acquisition (DIA)—particularly the SWATH-MS technique—has emerged as a prominent approach in quantitative proteomics, owing....

• • Advantages and Disadvantages of SWATH-MS

  What Is SWATH-MS? SWATH-MS is a mass spectrometry technique based on data-independent acquisition (DIA), first introduced by SCIEX. Unlike the traditional data-dependent acquisition (DDA) approach, SWATH-MS does not rely on on-the-fly precursor ion selection. Instead, it divides the full m/z scan range into a series of fixed-width windows and fragments all ions within each window, thereby systematically acquiring all detectable fragment ion spectra. Its core strengths include high throughput, excellent.....

• • SWATH-MS Data Analysis Workflow and Common Pitfalls

  Introduction: The Power of SWATH-MS Relies on Proper Data Analysis SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ion Spectra), a representative technique in data-independent acquisition (DIA), has significantly advanced large-scale, highly reproducible, and label-free quantitative proteomics. However, the intrinsic complexity of the data poses challenges, including intricate analysis workflows, strong parameter dependencies, and high variability in analytical outcomes. This article....

• • Application and Analysis of Advantages of SWATH-MS in Plasma Proteomics

  Plasma is among the most complex and research-relevant biological sample types. It carries protein signatures secreted from tissues throughout the body and is widely used in biomarker discovery, early disease diagnosis, and precision medicine due to its accessibility and high stability. However, plasma proteomics faces two major challenges: 1. An extremely wide dynamic range (>10¹⁰), with a small number of high-abundance proteins (e.g., albumin, globulin) accounting for over 90% of the total protein .......