Table II

Peptide statistics for Mascot searches performed with different search parameters

These are all performed with the same mouse liver dataset comprising the 4755 MS/MS queries acquired with the LTQ-FT. The Mascot significance threshold for the respective searches is shown in brackets.

Search parametersNo. of peptides (score >99% Mascot significance threshold)No. of peptides with score >24
Trypsin 2 MC,a 3 ppm1131 (26)1258
SemiTrypsin 2 MC, 3 ppm709 (37)1579
No Enzyme, 3 ppm474 (45)1761
Trypsin 2 MC, 2.0 Da490 (47)1767
No Enzyme, 2.0 Da193 (65)4205
Reverse db,b trypsin 2 MC 3 ppm17 (26)68
  • a MC, missed enzyme cleavage site.

  • b Reversed database search: 35 peptides with scores above 99% significance threshold. Of these, 18 are equivalent to peptide sequences identified in the forward search.