Resources

Proteomics Databases



Metabolomics Databases

• • De Novo Sequencing of Protein Drugs: Challenges and Breakthroughs

  Introduction: The “Sequence Blind Spot” of Protein Drugs With the rapid advancement of biopharmaceutical technologies, protein-based therapeutics—including monoclonal antibodies, fusion proteins, and recombinant enzymes—have emerged as a leading class in drug development. However, obtaining the complete sequence information of these protein drugs is a fundamental and critical task in various stages such as biosimilar development, quality consistency assessment, patent circumvention design, and .......

• • De Novo Protein Sequencing: How to Decode Unknown Proteins?

  In proteomics, clinical sample analysis, and studies involving non-model organisms, researchers increasingly face a recurring challenge: peptide fragments identified through mass spectrometry fail to match any known entries in existing databases. These sequences, termed “unknown proteins” or “orphan peptides,” may originate from: Previously unannotated proteins; Novel splice variants; Pathogen-derived, tumor-specific, or exogenously expressed proteins; Sequence deviations introduced by post-translational...

• • How to Use De Novo Sequencing for Antibody Structure Analysis?

  De Novo sequencing refers to determining amino acid sequences directly from protein samples based on MS/MS fragment ion data acquired using high-resolution mass spectrometry, without relying on any reference databases. The core of this technique lies in digesting the protein into numerous short peptides that collectively cover the full sequence, interpreting the corresponding fragment spectra with specialized algorithms, and assembling these sequences to reconstruct the full-length light and heavy chains...

• • Application of AQUA Technology in Protein Research

  With life science research increasingly shifting toward precision and quantitative analysis, the importance of proteins as functional biomolecules has become more pronounced. Whether investigating disease mechanisms or developing therapeutic strategies, the accurate determination of protein expression levels and their dynamic changes is a critical prerequisite for scientific discovery. AQUA (Absolute Quantification), an absolute quantification mass spectrometry method based on stable isotope-labeled........

• • Applications and Challenges of SILAC Labeling in Quantitative Proteomics

  In quantitative proteomics, the ability to accurately and reproducibly measure protein abundance changes across different samples is crucial for uncovering underlying biological mechanisms. Stable Isotope Labeling by Amino acids in Cell culture (SILAC), a well-established metabolic labeling technique, introduces heavy isotope-labeled amino acids during cell growth, enabling high-precision and systematic quantification of proteins. This paper discusses the applications of SILAC in quantitative proteomics....

• • iTRAQ Quantification Technology: Principles, Advantages, and Applications

  In proteomics research, the accurate and sensitive comparison of protein abundance across different samples is crucial for elucidating underlying biological mechanisms. iTRAQ (Isobaric Tags for Relative and Absolute Quantitation), a mass spectrometry-based multiplex quantification technique, has become a pivotal tool in life sciences due to its high throughput, precision, and wide applicability. This paper systematically introduces the principles, key advantages, and major applications of iTRAQ technology.

• • Applications of LC-MS in Quantitative Proteomics

  Proteomics, a critical branch of life sciences, aims to comprehensively elucidate the expression, modification, and interactions of proteins within cells, tissues, or organisms. Quantitative proteomics further advances biomedical research, drug discovery, and the investigation of disease mechanisms. Among the analytical techniques employed, Liquid Chromatography–Mass Spectrometry (LC-MS/MS) has emerged as a central tool in quantitative proteomics due to its high sensitivity, high throughput, and extensive..

• • Mass Spectrometry-Based Quantitative Proteomics Analysis: Principles and Applications

  In the post-genomic era, quantitative proteomics has become an essential tool for deciphering the complexity of biological systems, elucidating disease mechanisms, and identifying biomarkers. Among various approaches, mass spectrometry-based quantitative proteomics stands out due to its high sensitivity, large throughput, and accurate quantification, making it widely applicable in both basic research and biopharmaceutical development. This review systematically summarizes the fundamental principles.......

• • Comparison of Protein Quantification Methods: iTRAQ, SILAC, AQUA, and Label-Free Quantification Techniques

  In contemporary life science research, protein quantification serves as a crucial tool for elucidating biological mechanisms, identifying disease biomarkers, and investigating drug mechanisms of action. Compared to conventional protein expression analysis techniques such as Western blotting and ELISA, mass spectrometry (MS)-based quantitative proteomics offers distinct advantages, including high throughput, superior sensitivity, and strong multiplexing capabilities. As a result, it has become a core .......

• • How to Master De Novo Sequencing and Achieve Accurate Protein Identification

  De novo sequencing is a crucial technique in proteomics research, particularly applicable to biological systems that lack reference databases or contain unknown protein variants. In contrast to database-dependent mass spectrometry identification, de novo sequencing deciphers peptide ion information directly from mass spectrometry data to deduce amino acid sequences, thereby enabling more comprehensive and precise protein identification. Principles and Advantages of De Novo Sequencing De novo sequencing.....