Resources

Proteomics Databases



Metabolomics Databases

• • Key Technologies and Challenges in De Novo Sequencing

  In proteomics research, spectral data are typically interpreted by matching them against existing protein databases. However, in advanced applications such as studies of non-model organisms, the discovery of novel protein modifications, single-cell proteomics, and antibody characterization, these databases often fail to provide adequate coverage. As a result, de novo peptide sequencing has emerged as a critical technique for deciphering unknown protein sequences. De novo sequencing is a methodology that....

• • Advantages and Applications of De Novo Sequencing

  In proteomics research, the majority of mass spectrometry data analysis relies on database search approaches, which match experimental spectra with known protein sequences. De novo sequencing, a methodology that does not depend on any reference databases, has emerged as a powerful tool for elucidating previously unknown protein structures and functions. Core Advantages of De Novo Sequencing 1. Fully Independent of Reference Databases De novo sequencing derives peptide amino acid sequences directly from.....

• • What Is Protein Quantification Assay?

  Protein quantification refers to the process of measuring the amount or relative abundance of proteins in a given sample. This assay plays a crucial role in proteomics, biomarker discovery, and elucidation of drug mechanisms. By quantifying protein expression under different conditions, researchers can gain deeper insights into cellular function, disease progression, and therapeutic responses. Main Types of Protein Quantification Assays 1. Total Protein Quantification This is the most fundamental form of...

• • De Novo Peptide Sequencing via Tandem Mass Spectrometry

  In proteomics research, database-dependent mass spectrometry data analysis (database search) has become the predominant approach. However, in emerging fields such as non-model organisms, natural products, antibody engineering, and novel peptide therapeutics, the absence or incompleteness of reference databases limits the applicability of traditional methods. In such cases, de novo peptide sequencing—a technique that reconstructs peptide amino acid sequences directly from mass spectrometry data without......

• • Protein Quantification Technologies: Methods, Advantages, and Applications

  In contemporary biomedical research, proteins are considered direct effectors of cellular function. Whether investigating the molecular mechanisms underlying diseases or developing strategies in precision medicine, researchers must gain a deep understanding of how protein expression changes under varying conditions. As such, protein quantification technologies have become an indispensable component of modern life science research. Scientific Significance of Protein Quantification Protein quantification.....

• • Mass Spectrometry Protein Quantification Analysis for Drug Discovery

  Mass spectrometry (MS), a highly sensitive and specific analytical technique, plays a critical role in life sciences, particularly in drug discovery. When integrated with quantitative proteomics, MS contributes significantly to the identification of novel drug targets, elucidation of molecular mechanisms, and assessment of drug efficacy. Overview of Mass Spectrometry Protein Quantification Analysis 1. Definition of Mass Spectrometry Protein Quantification Analysis Mass spectrometry protein quantification...

• • Label-Free Protein Quantification Methods: Advantages and Limitations

  In contemporary life sciences research, proteomics is transitioning from a focus on “qualitative identification” to a new phase emphasizing “quantitative analysis.” Quantitative proteomics enables the investigation of dynamic changes in protein expression levels under varying treatment conditions, thereby allowing researchers to gain deeper functional insights into biological processes. Among the various quantitative proteomic approaches, Label-Free Quantification (LFQ) has emerged as one of the fastest....

• • Analysis of Advantages and Limitations of Different Protein Quantification Methods

  Protein quantification is a critical step in life science research, as it directly impacts the elucidation of biological processes and the understanding of disease mechanisms. With ongoing advancements in mass spectrometry and sample preparation techniques, various protein quantification methods have been developed. Labeling-based Quantification Labeling-based quantification methods utilize isotopic or isobaric tags introduced during sample processing to enable relative or absolute quantification across....

• • Understanding iTRAQ, SILAC, and Label-Free Quantification: Differences, Advantages, and Limitations

  In proteomics research, accurate protein quantification plays a central role in elucidating the dynamic changes within biological systems. With the advancement of mass spectrometry technologies, iTRAQ, SILAC, and Label-Free Quantification (LFQ) have emerged as three widely adopted quantitative strategies, each offering distinct features suitable for various experimental scenarios. iTRAQ: Isobaric Labeling for High-Throughput Multi-Sample Comparison 1. Principle Overview iTRAQ (Isobaric Tags for Relative....

• • How to Choose the Right Protein Quantification Technique: iTRAQ vs SILAC

  In proteomics research, accurate protein quantification techniques are fundamental to elucidating changes in biological processes. iTRAQ and SILAC, as two widely adopted quantification techniques, each offer distinct advantages and limitations. A thorough understanding of their underlying principles, application contexts, and key differences is essential for designing efficient and robust experimental workflows. Fundamental Principles of iTRAQ and SILAC 1. Overview of iTRAQ Technique iTRAQ (Isobaric Tags...