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 |