Does Mass Spectrometry Identify Specific Amino Acid Sequences?

Proteomics Mass Spectrometry refers to the use of mass spectrometry technology to analyze the mass of proteins or polypeptides, in order to identify their amino acid sequence. Both in theory and in practice, mass spectrometry can provide specific amino acid sequence information of proteins or polypeptides. This is achieved by measuring the mass of polypeptides and the mass of fragment ions generated in the mass spectrometer.

 

In mass spectrometry analysis, proteins or polypeptides are first cut into shorter segments by enzymes (such as trypsin), and then these fragments are ionized in the mass spectrometer, making them charged and capable of moving in a magnetic field. The mass spectrometer measures the mass/charge ratio (m/z value) of these charged particles, generating a spectrum. By analyzing the peak values on the spectrum, scientists can determine the mass of the peptide segments, and by further tandem mass spectrometry (MS/MS) experiments, they can also determine the mass of fragment ions. These data together can be used to infer the original amino acid sequence of proteins or polypeptides.

 

For accurate identification of different amino acids, their mass differences and the formation of fragment ions in the mass spectrometer need to be considered. Although most amino acids can be identified by their unique mass differences, some amino acids such as leucine and isoleucine have the same mass, so more advanced techniques and strategies are needed to distinguish.

 

In some cases, mass spectrometry may not provide a complete amino acid sequence, especially when analyzing large proteins or highly modified proteins. Therefore, mass spectrometry data usually need to be combined with bioinformatics analysis, such as database search or de novo sequence analysis, to help determine the complete sequence of the protein.