Resources

Proteomics Databases



Metabolomics Databases

• • Is Mass Spec for Proteins Only

  Mass spectrometry (MS) is a powerful analytical tool that identifies and quantifies molecular components in samples by measuring their mass-to-charge ratio (m/z). While its utility in protein analysis is well established, MS applications extend significantly beyond proteomics. Below are key areas where MS has proven invaluable:   Metabolomics Metabolomics leverages MS to investigate small molecular metabolites, such as carbohydrates, lipids, amino acids, and nucleotides, providing insights into metabo......

• • What Proteins Indicate MS?

  Mass spectrometry (MS) is a powerful tool for protein detection, enabling the determination of protein mass, as well as the assessment of protein purity and consistency. Common MS techniques, such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), are used in top-down and bottom-up approaches, respectively. In the top-down approach, intact proteins are directly analyzed, while the bottom-up approach involves enzymatic digestion (e.g., trypsin digestion) to produc......

• • What is Phosphoproteomics

  Phosphoproteomics, a specialized branch of proteomics, focuses on investigating protein phosphorylation modifications within organisms and their roles in biological processes. Phosphorylation involves the addition of a phosphate group (PO4) to specific amino acid residues, most commonly serine (Ser), threonine (Thr), and tyrosine (Tyr).   This modification profoundly influences protein functions, regulating activity, stability, intracellular localization, and interactions with other proteins. Phosphor......

• • De Novo Protein Sequencing

  Principle of De Novo Protein Sequencing De novo protein sequencing determines the amino acid sequence of proteins without relying on existing DNA or protein databases. This technique is based on the predictable fragmentation patterns of peptides during mass spectrometry. Specific cleavage patterns are identified, and the mass differences between peaks in the spectrum are used to deduce amino acid sequences and identify post-translational modifications. During fragmentation, peptides produce various io......

• • 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......