Resources

• • Can Mass Spectrometry Determine Protein Structure?

  In protein research, determining protein structure is critical for understanding its function, interactions, and role in diseases. As a powerful analytical tool, mass spectrometry has become an increasingly important method in protein studies. But can mass spectrometry determine protein structure?   Traditionally, X-ray crystallography and nuclear magnetic resonance (NMR) have been the primary techniques for determining protein structures. X-ray crystallography provides high-resolution three-dimension......

• • What are the Two Methods in Protein Identification by Mass Spectrometry?

  Protein identification is a critical component of proteomics, and mass spectrometry (MS) is one of the most essential techniques for this purpose. Below, two commonly used MS methods for protein identification are described:   Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) 1. Technical Principles In MALDI-TOF MS, protein samples are mixed with a matrix, and then subjected to laser irradiation. This process generates gas-phase ions from the sample and matrix......

• • Can Mass Spectrometry be Used for Protein Sequencing?

  Protein sequencing directly reveals the amino acid sequence of proteins, which is essential for understanding their structure and function. With the amino acid sequence determined, the three-dimensional structure of the protein can be predicted, which facilitates the understanding of its biological roles and interaction mechanisms. This is crucial for studying biological processes and disease mechanisms. Current protein sequencing technologies include de novo mass spectrometry sequencing, Edman degrad......

• • 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......