Resources

Proteomics Databases



Metabolomics Databases

• • De Novo Peptide Sequencing

  De novo peptide sequencing enables researchers to determine the amino acid sequences of peptides or proteins without relying on a reference sequence. This technology has significantly advanced our understanding of protein diversity and complexity, particularly in the analysis of unknown, variant, or non-model organism proteins, demonstrating its distinct advantages.   De novo peptide sequencing integrates mass spectrometry with computational algorithms. The technique utilizes mass spectrometry for hig......

• • What is the Edman Reaction?

  The Edman reaction, also known as the Edman degradation, is a method for sequencing amino acids in proteins or peptides. The Edman reaction is an analytical technique used to determine the N-terminal amino acid sequence of proteins or polypeptides. It works through a series of chemical reactions that sequentially reveal the amino acid composition at the protein's N-terminus. In the first step of the Edman reaction, phenylisothiocyanate (PITC) reacts with the N-terminal amino group and the amino group ......

• • Can Edman Sequencing be Performed in Complex Mixtures?

  The Edman sequencing method is widely used to determine the primary structure of proteins, specifically the unique sequence of amino acids in the protein chain. The Shimadzu Protein N-terminal Sequencer (PPSQ) is one such device employed for this purpose. Each protein has a distinct and defined amino acid sequence, and Edman sequencing plays a key role in decoding this sequence. This technique is crucial for protein characterization and is often the first step in understanding a protein’s functional p......

• • Can Mass Spectrometry be Used for Proteins?

  In life sciences, proteins—essential mediators of biological processes—are studied intensively to understand their structures, functions, and interactions. Advances in technology have introduced numerous high-throughput, high-precision techniques, with mass spectrometry emerging as a particularly valuable tool in protein analysis.   Mass spectrometry identifies and characterizes molecules by measuring the mass-to-charge ratio (m/z) of ions. By ionizing sample molecules and separating them within elect......

• • Why is Phosphoproteomics Still a Challenge?

  With the rapid advancements in biotechnology, proteomics has emerged as a pivotal area in life sciences. Protein phosphorylation, one of the most critical covalent modifications, has a profound influence on essential biological processes, including cell proliferation, differentiation, signal transduction, and apoptosis. Despite its great potential to uncover biological insights and accelerate drug development, phosphoproteomics still presents substantial research challenges.   Complexity......

• • What is the Function of Phosphoproteins?

  The function of phosphoproteins has a wide range of applications, including medicine, agriculture. In medicine, phosphoproteomics is indispensable for understanding complex biological networks, elucidating disease mechanisms, identifying and validating biomarkers, guiding personalized treatment strategies, and advancing drug discovery. In agriculture, protein phosphorylation is vital for regulating plant growth and development and for studies on environmental adaptability.   A phosphoprotein is a prot......

• • What is Peptide Sequencing?

  Peptide sequencing is a fundamental biochemical method designed to precisely determine the order of amino acids within a peptide chain. Peptides, the essential building blocks of proteins, are short chains of amino acids linked by peptide bonds. These small proteins have diverse biological functions, including roles in hormone signaling and enzymatic catalysis. Accurate peptide sequencing allows researchers to investigate the specific mechanisms, structural characteristics, and biological roles of the......

• • How is Peptide Sequencing Performed?

  Peptide sequencing serves as a critical technique for uncovering the structural and functional information encoded within polypeptides, which are essential to various biological processes.   Polypeptides, formed by multiple amino acids linked via peptide bonds, require sequencing to identify their precise amino acid arrangement. This sequencing is analogous to solving a complex puzzle, where each method leverages unique chemical and physical principles to determine amino acid order. For instance, mass......

• • In What Ways is Mass Spectrometry Employed in Proteomics Research?

  Mass spectrometry (MS) is a cornerstone of proteomics research, enabling comprehensive analysis of protein expression, modifications, and interactions within biological systems. Its applications extend beyond individual protein characterization to encompass global insights into proteomic dynamics. Key areas of application include: Proteome Quantification MS provides quantitative insights into protein expression across entire proteomes, offering a comprehensive view of protein abundance in cells, tissu......

• • What Makes ESI MS/MS an Optimal Approach for Protein Identification?

  Electrospray ionization tandem mass spectrometry (ESI MS/MS) is a powerful analytical method that combines electrospray ionization (ESI) and tandem mass spectrometry (MS/MS). It has become a preferred choice for protein identification due to its unique advantages across multiple dimensions: Gentle Ionization for Biomolecules ESI employs a soft ionization process where sample solutions are nebulized into charged droplets under an electric field and auxiliary gas flow. As these droplets evaporate, small......