Resources

Proteomics Databases



Metabolomics Databases

• • How Can SPS-MS3 Be Utilized to Optimize TMT Workflows and Minimize Ratio Compression?

  Tandem Mass Tags (TMT) are an isotope-labeling technology widely employed in high-throughput quantitative proteomics, enabling parallel analysis of multiple samples (currently supporting up to 18-plex). This approach has demonstrated substantial advantages in elucidating disease mechanisms, understanding drug modes of action, and identifying clinical biomarkers. However, ratio compression remains one of the most critical technical bottlenecks in TMT quantification. Co-eluting peptides at the MS2 stage......

• • How to Choose the Appropriate TMT Quantification Platform?

  As proteomics research advances, researchers are increasingly confronted with larger sample sizes, particularly in application scenarios such as integrated multi-omics analysis, disease cohort studies, and drug screening. This has driven a growing demand for quantitative techniques that combine high throughput with high accuracy. Among the available strategies, tandem mass tag (TMT)–based quantification has emerged as one of the most widely adopted approaches in quantitative proteomics, owing to its e......

• • What Is 4D Proteomics?

  With the rapid advancement of proteomics technologies, the demand for greater depth, breadth, and accuracy in data acquisition has significantly increased. Conventional three-dimensional mass spectrometry (MS) approaches have enabled large-scale protein identification and quantification; however, they face limitations such as insufficient resolution and low signal-to-noise ratios when analyzing complex samples, low-abundance proteins, or structurally similar peptides. To address these challenges, four......

• • How Can Enzyme Activity Be Quantitatively Analyzed Using ABPP?

  In biological research, proteomic measurements of enzyme expression levels are often used to infer functional states. However, expression abundance does not necessarily reflect catalytic activity. Enzymes may exist in inactive forms, be regulated by inhibitors, or undergo post-translational modifications that modulate their function. Therefore, enzyme activity represents the critical indicator of their true functional status. Activity-Based Protein Profiling (ABPP) employs chemical probes to selective......

• • How Can ABPP Address the Functional Limitations of Transcriptomics?

  In the current era of increasingly comprehensive multi-omics data, transcriptomics remains one of the principal approaches to elucidate gene regulatory mechanisms. Technologies such as RNA-Seq enable researchers to systematically characterize gene transcription under diverse conditions. Nevertheless, the assumption that expression equates to function faces an inherent limitation: changes at the transcriptional level do not necessarily correspond to alterations in protein activity. This is precisely th......

• • How to Perform Untargeted Metabolomics?

  Untargeted metabolomics refers to the comprehensive analysis of thousands of metabolites in biological samples using high-resolution mass spectrometry techniques (e.g., LC-MS/MS or GC-MS), without predefining target compounds. This approach aims to capture metabolic perturbations arising from disease, environmental changes, or pharmacological interventions. Untargeted metabolomics is a small-molecule profiling strategy designed to systematically detect as many metabolites as possible in a given sample......

• • Application of Protein Sequence Analysis in Structure–Function Prediction

  Proteins represent the fundamental functional molecules of biological systems, with structure and function being intrinsically interdependent. With the rapid advancement of high-throughput sequencing technologies, the volume of protein sequence data has expanded exponentially. The efficient interpretation of sequence information, along with the prediction of protein three-dimensional structures and associated biological functions, has therefore emerged as a central challenge in life sciences. This art......

• • How TIMS Technology Improves Depth in 4D Proteomics Analysis?

  Proteomics, as a pivotal analytical methodology for elucidating life processes and disease mechanisms, has witnessed substantial advancements in recent years. Particularly in areas such as the investigation of low-abundance proteins, biomarker discovery, and the elucidation of signaling pathways, researchers have set increasingly stringent demands on the depth of protein identification. Here, identification depth not only denotes the total number of identifiable proteins but also reflects the capacity......

• • Key Applications of Protein Purity Analysis in Therapeutic Protein Development

  In the development of therapeutic proteins, including monoclonal antibodies, recombinant proteins, and fusion proteins, protein purity analysis constitutes not only a fundamental aspect of product quality but also a critical step for ensuring drug safety, therapeutic efficacy, and successful regulatory approval. Ensuring Drug Safety 1. Minimizing Immunological Risks Insufficient protein purity often indicates the presence of contaminating proteins, degradation products, or aggregates, which may elici......

• • How to Perform Shotgun Proteomics Using Tandem Mass Spectrometry (MS/MS)?

  In contemporary proteomics, shotgun proteomic analysis integrated with tandem mass spectrometry (MS/MS) enables the high-throughput identification and relative quantification of thousands of proteins within complex biological systems. This approach is extensively applied in basic research, elucidation of disease mechanisms, and biomarker discovery. Here, we provide a systematic overview of the conceptual framework and methodological details of MS/MS-based shotgun proteomics, offering both theoretical ......