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Table 6 For MsPI 1, Mascot 1 and Piums the mass tolerance was set to 0.3 Da; in the other cases it was set to 100 ppm. For MsPI 1, MsPI 2 and MsPI 3, score 1, 2 and 3 were respectively used with uniform distribution. For each band the position of the "true" protein in the significant candidate list, the length of that list either using or not using the knowledge about the MW of the band, the MW and the pI of the "true" protein, the number of matching masses and the sequence coverage are reported.

From: A Perl procedure for protein identification by Peptide Mass Fingerprinting

Gel band (#) Software tool Rank (# significant proteins without MW filtering) Rank (# significant proteins with MW filtering) MW (Da) pI Matches (#) Coverage (%)
1 MsPI 1 2 (2) 1 (1) 123852 5.31 23 0.267
  MsPI 2 7 (8) 1 (1) 123852 5.31 23 0.270
  MsPI 3 2 (2) 1 (1) 123852 5.31 23 0.267
  Mascot 1 1 (1) 1 (1) 124292 5.50 23 0.250
  Mascot 2 1 (1) 1 (1) 124292 5.50 23 0.250
  Piums - - (-) - - 21 0.242
2 MsPI 1 1 (2) 1 (1) 191785 5.32 36 0.252
  MsPI 2 1 (4) 1 (1) 191785 5.32 35 0.252
  MsPI 3 1 (2) 1 (1) 191785 5.32 35 0.252
  Mascot 1 1 (1) 1 (1) 193260 5.48 36 0.250
  Mascot 2 1 (3) 1 (1) 193260 5.48 35 0.250
  Piums 1 (1) - - - 36 0.257
3 MsPI 1 2 (8) 1 (1) 104981 5.08 21 0.245
  MsPI 2 - (4) - (-) 104981 5.08 21 0.245
  MsPI 3 2 (4) 1 (1) 104981 5.08 21 0.245
  Mascot 1 1 (2) 1 (1) 105245 5.27 21 0.240
  Mascot 2 1 (6) 1 (2) 105245 5.27 21 0.240
  Piums - (-) - - - 19 0.254
4 MsPI 1 2 (4) 1 (1) 95382 6.38 20 0.286
  MsPI 2 1 (5) 1 (1) 95382 6.38 20 0.286
  MsPI 3 1 (6) 1 (2) 95382 6.38 20 0.286
  Mascot 1 1 (1) 1 (1) 96246 6.41 22 0.320
  Mascot 2 1 (1) 1 (1) 96246 6.41 22 0.320
  Piums - (-) - - - 19 0.341
5 MsPI 1 2 (8) 2 (3) 84351 4.70 28 0.418
  MsPI 2 3 (3) 2 (2) 84351 4.70 28 0.418
  MsPI 3 2 (12) 2 (3) 84351 4.70 28 0.418
  Mascot 1 1 (2) 1 (2) 83554 4.97 35 0.480
  Mascot 2 1 (3) 1 (2) 83554 4.97 34 0.480
  Piums 1 (1) - - - 28 0.364
6 MsPI 1 2 (8) 1 (1) 67900 7.37 24 0.515
  MsPI 2 - (1) - (-) 67900 7.37 23 0.509
  MsPI 3 1 (6) 1 (1) 67900 7.37 23 0.509
  Mascot 1 1 (2) 1 (1) 68519 7.58 24 0.510
  Mascot 2 1 (4) 1 (2) 68519 7.58 23 0.500
  Piums - (-) - - - 19 0.446
7 MsPI 1 1 (3) 1 (1) 53146 4.82 21 0.468
  MsPI 2 1 (2) 1 (1) 53146 4.82 21 0.468
  MsPI 3 1 (2) 1 (1) 53146 4.82 21 0.468
  Mascot 1 1 (1) 1 (1) 53676 5.06 21 0.500
  Mascot 2 1 (3) 1 (1) 53676 5.06 21 0.500
  Piums - (-) - - - 16 0.413
8 MsPI 1 - (2) - (-) 49674 4.53 8 0.232
  MsPI 2 - (1) - (-) 49674 4.53 8 0.232
  MsPI 3 - (1) - (-) 49674 4.53 8 0.232
  Mascot 1 - (-) - (-) 50095 4.78 8 0.230
  Mascot 2 - (-) - (-) 50095 4.78 8 0.230
  Piums - (-) - - - 8 0.232
9 MsPI 1 1 (4) 1 (1) 45982 9.79 31 0.784
  MsPI 2 1 (4) 1 (1) 45982 9.79 32 0.787
  MsPI 3 1 (5) 1 (1) 45982 9.79 32 0.787
  Mascot 1 1 (1) 1 (1) 46180 9.45 31 0.730
  Mascot 2 1 (1) 1 (1) 46180 9.45 31 0.730
  Piums 1 (1) - - - 27 0.715
10 MsPI 1 1 (9) 1 (2) 41611 5.10 13 0.349
  MsPI 2 2 (5) 2 (2) 41611 5.10 13 0.379
  MsPI 3 1 (6) 1 (4) 41611 5.10 13 0.379
  Mascot 1 1 (4) 1 (4) 42052 5.29 13 0.370
  Mascot 2 1 (4) 1 (4) 42052 5.29 13 0.370
  Piums 2 (2) - - - 13 0.380