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Table 1 Characteristics of peptide products following digestion of the yeast proteome with different agents.

From: In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

  Endo AspN CNBr Chymotrypsin Trypsin* (no missed cleavages) Trypsin (zero or one missed cleavages) Trypsin (zero, one or two missed cleavages) Trypsin and chymo-trypsin
Total number of peptides in proteome 150,427 59,702 216,969 291,203 593,88 930,613 411,401
Mean peptide mass (isotopic) 2192.5 5554.2 1496.7 1229.2 1637.4 2078.5 614.1
Mean number of peptides per protein 24.2 9.6 35.0 41.9 95.7 150.0 66.3
  1. *Idealized digestion criteria were used (in the laboratory, the rules governing cleavage may be more complex – for instance trypsin rarely cuts after arginine or lysine when the distal residue is proline). Here, the criteria used were: EndoAspN (X-D), CNBr (X-M), Chymotrypsin (X-L, X-F, X-Y, X-W), trypsin (K-X, R-X).