Peptide Spectrum Analysis

Peptide spectrum analysis is a key concept in mass spectrometry, mainly used for the identification of proteins and their degradation products - peptides. In mass spectrometry analysis, protein samples are first hydrolyzed into smaller peptides by enzymes (such as trypsin), and then these peptides are analyzed by mass spectrometry. The peptide spectrum is a graphical representation of mass spectrometry data, displaying the mass-to-charge ratio (m/z) of the ions detected in the mass spectrometry analysis and their relative intensity.

 

Peptide spectrum analysis can be used for qualitative research (determining the existence of specific proteins) and quantitative research (measuring the abundance of specific proteins). Qualitative analysis focuses on identifying proteins through the mass-to-charge ratio of peptide fragments and their fragmentation spectra, while quantitative analysis requires more precise measurement of the peak area or height of specific ions, which usually involves more complex data processing. Interpreting peptide spectra requires the ability to identify different types of fragment ions and to reconstruct the original peptide's amino acid sequence based on this information. Moreover, any unusual mass shifts may indicate the presence of post-translational modifications (such as phosphorylation, acetylation, etc.), which require additional verification steps.

 

Due to the complexity of peptide spectrum data, specialized software tools are often needed to assist in the analysis. These tools use various algorithms to match the experimentally generated peptide spectrum with the theoretical peptide spectrum (predicted based on known protein sequences), thus identifying the proteins in the sample. The software can also help correct instrument errors, identify potential post-translational modifications, and conduct quantitative analysis.