Figure 2. Peptide identification strategies.

Peptide identification can be performed by correlating acquired experimental MS/MS spectra with theoretical spectra predicted for each peptide contained in a protein sequences database (database search approach), or against spectra from a spectral library (spectral library search). Alternatively, peptide sequences can be extracted directly from the spectra using de novo sequencing. Hybrid approaches such as sequence tag-assisted database search start by extracting short tags (length 3 in this illustration) followed by database searching in which the list of candidate peptides is restricted to those peptides only that contain one of the sequence tags extracted from the spectrum.