Resources

Proteomics Databases



Metabolomics Databases

• • Principle of Peptide Sequencing by Mass Spectrometry

  Mass spectrometry (MS) is a critical analytical technique in contemporary biological research, extensively utilized in proteomics, metabolomics, and clinical diagnostics. Peptide sequencing by mass spectrometry involves detecting and analyzing protein samples with a mass spectrometer to determine their peptide sequences.

• • Advantages and Disadvantages of Peptide Sequencing by Mass Spectrometry

  Mass spectrometry (MS) is an essential analytical tool in modern biological research, widely used in proteomics studies. MS sequencing identifies and quantifies peptide sequences by measuring the mass-to-charge ratio (m/z) of ionized molecules. Despite the numerous advantages of MS sequencing in peptide sequence analysis, it also presents certain challenges and limitations.

• • Protein Phosphorylation Site Detection

  Protein phosphorylation is a core event in cell signal transduction, playing a crucial role in many biological processes, such as cell cycle, proliferation, differentiation, and metabolism. To deeply understand these processes, it is key to determine which proteins are phosphorylated and the precise phosphorylation sites. In recent years, the scientific community has developed a variety of techniques to address this challenge.

• • Common Post-Translational Modifications of Proteins

  Post-translational modification (PTM) refers to the biochemical processes in which amino acid residues in proteins are chemically modified after translation. These chemical modifications greatly expand the functional diversity of proteins, allowing them to participate in various cellular physiological processes.

• • Extinction Coefficient Measurement Method

  The molar extinction coefficient is a unit of measurement that assesses the absorption intensity of a specific wavelength of light by a chemical substance. The molar extinction coefficient of proteins at 280nm is mostly determined by the number of aromatic residues, particularly tryptophan, and can be predicted based on the amino acid sequence. If the molar extinction coefficient is known, it can be used to determine the concentration of protein in a solution.

• • Amino Acid Sequence Determination Methods

  Amino acid sequence determination, also known as protein sequence determination, refers to the process of determining the exact order of amino acid residues in a protein. This information is vital for understanding the structure and function of proteins, identifying new proteins, studying protein interactions, and disease associations.

• • N-Glycosylation Site Analysis

  N-glycosylation is an important protein modification, mainly involving the covalent bond connection between the nitrogen atom of amino acids on proteins and sugar molecules. N-glycosylation typically occurs on the nitrogen atom of asparagine, with the specific sequence pattern being Asn-X-Ser/Thr, where X is any amino acid except proline.

• • Circular Dichroism Spectroscopy for Protein Determination

  Circular Dichroism (CD) is a spectroscopic measurement based on the optical isomerism of plane-polarized light by optically active substances. When plane-polarized light passes through an optically active substance, its two orthogonal oscillation components are absorbed differently, resulting in elliptically polarized light.   CD spectra provide information on the structure and conformational changes of proteins, polypeptides, and other optically active molecules.

• • Ubiquitination Site Detection

  Ubiquitination site detection is an analytical technique used in biological research to identify specific amino acid residues on protein molecules that undergo ubiquitination modification. Ubiquitination is a common protein modification process, where ubiquitin protein covalently attaches to specific residues of the target protein, usually lysine residues.

• • Advantages and Disadvantages of Peptide Mass Fingerprinting

  Peptide mass fingerprinting (PMF) is a cornerstone technique in the field of proteomics, enabling the identification and characterization of proteins with remarkable precision. This method relies on mass spectrometry to generate a unique peptide mass pattern from protein digests, which is then matched against theoretical spectra in protein databases. While PMF has significantly advanced our ability to study proteomes, it is not without its limitations.