Does proteomics mass spectrometry provide specific amino acid sequences?

Proteomics Mass Spectrometry sequencing actually refers to the use of mass spectrometry technology for the mass analysis of proteins or peptides to identify their amino acid sequences. In theory and practice, mass spectrometry can provide specific amino acid sequence information for proteins or peptides. This is achieved by measuring the mass of the peptide and the mass of fragment ions generated in the mass spectrometer.

In mass spectrometry analysis, proteins or peptides are first cleaved into shorter fragments by enzymes such as trypsin. These fragments are then ionized in the mass spectrometer, allowing them to carry a charge and move in a magnetic field. The mass spectrometer measures the mass-to-charge ratio (m/z value) of these charged particles, generating a spectrum. By analyzing the peaks on the spectrum, scientists can determine the mass of the peptide segments. Through further tandem mass spectrometry (MS/MS) experiments, they can also determine the mass of fragment ions, and this data collectively can be used to deduce the amino acid sequence of the original protein or peptide.

For accurate identification of different amino acids, their mass differences and the formation of fragment ions in mass spectrometry must be considered. Although most amino acids can be recognized by their unique mass differences, some amino acids, such as leucine and isoleucine, have the same mass, necessitating more advanced techniques and strategies to distinguish them.

In some cases, mass spectrometry may not provide a complete amino acid sequence, especially when analyzing large or highly modified proteins. Therefore, mass spectrometry data often needs to be combined with bioinformatics analysis, such as database searches or de novo sequencing analysis, to assist in determining the complete sequence of a protein.

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