De Novo
Interpretation of MS/MS Spectra and Protein Identification via Database
Searching
SHENG Quan-Hu, XIE Tao, DING Da-Fu*
( Shanghai Institute of Biochemistry, the Chinese Academy of Sciences,
Shanghai 200031, China )
Abstract Peptide
sequencing via tandem mass spectrometry(MS/MS)is one of the most powerful tools
in proteomics to identify proteins. A new algorithm was developed for de
novo interpretation of MS/MS spectra using graph theory and dynamic
alignment between real spectra and theoretical spectra. The trustworthy
peptides from de novo interpretation were used in protein
identification via database searching. A high throughput statistical analysis
of SwissProt and TrEMBL protein databases showed that it’s enough to identify a
protein in database with three sequence tags of four amino acid residues, two
sequence tags of five amino acid residues or one sequence tag of eight amino
acid residues.
Key words proteome；tandem mass spectrometry；protein identification；database
*Corresponding author：Tel,86-21-64374430-254；Fax,86-21-64338357；e-mail, [email protected]