Table 2 Performance comparison of msInspect, MZmine 2, Progenesis LC-MS, and XCMS.
From: Using a spike-in experiment to evaluate analysis of LC-MS data
msInspect (Number of selected features = 2099, sensitivity = 9/13, FP = 2090) | ||||
|---|---|---|---|---|
Feature No. | Peptide | m / z (charge) | q -value (rank) | FC (rank) |
1 | RGDSPASSKP | 501.25 (2) | 0.0139 (38) | Inf (1) |
2 | DRVYIHP | 450.23 (2) | 0.0114 (1) | Inf (1) |
3a | RPPGFSPFR | 530.78 (2) | 0.0164 (43) | 90.5 (1911) |
3b | RPPGFSPFR | 354.19 (3) | 0.0114 (1) | 32.5 (1935) |
4 | DRVYIHPF | 523.77 (2) | 0.0166 (220) | 47.8 (1921) |
5a | DRVYIHPFHL | 648.84 (2) | 0.0120 (28) | Inf (1) |
5b | DRVYIHPFHL | 432.89 (3) | 0.0126 (31) | Inf (1) |
6 | DRVYIHPFHLLVYS | 586.98 (3) | 0.0164 (43) | Inf (1) |
7a | WLTGPQLADLYHSLMK | 624.99 (3) | Â | Â |
7b | WLTGPQLADLYHSL(M)K | 630.35 (3) | 0.0164 (43) | Inf (1) |
8 | YPIVSIEDPFAEDDWEAWSHFFK | 943.43 (3) | Â | Â |
9a | GIGAVLKVLTTGLPALISWIKRKRQQ | 712.43 (4) | Â | Â |
9b | GIGAVLKVLTTGLPALISWIKRKRQQ | 570.15 (5) | Â | Â |
MZmine 2 (Number of selected features = 539, sensitivity = 7/13, FP = 532) | ||||
Feature No. | Peptide | m/z (charge) | q-value (rank) | FC (rank) |
1 | RGDSPASSKP | 501.25 (2) | 0.0278 (18) | 40.0 (243) |
2 | DRVYIHP | 450.23 (2) | 0.0271 (1) | 97.9 (152) |
3a | RPPGFSPFR | 530.78 (2) | 0.0271 (1) | 54.1 (202) |
3b | RPPGFSPFR | 354.19 (3) | 0.0271 (1) | 41.4 (238) |
4 | DRVYIHPF | 523.77 (2) | 0.0278 (18) | 204.9 (107) |
5a | DRVYIHPFHL | 648.84 (2) | 0.0399 (173) | 11.2 (509) |
5b | DRVYIHPFHL | 432.89 (3) | 0.0301 (53) | 9636.3 (34) |
6 | DRVYIHPFHLLVYS | 586.98 (3) | Â | Â |
7a | WLTGPQLADLYHSLMK | 624.99 (3) | Â | Â |
7b | WLTGPQLADLYHSL(M)K | 630.35 (3) | Â | Â |
8 | YPIVSIEDPFAEDDWEAWSHFFK | 943.43 (3) | Â | Â |
9a | GIGAVLKVLTTGLPALISWIKRKRQQ | 712.43 (4) | Â | Â |
9b | GIGAVLKVLTTGLPALISWIKRKRQQ | 570.15 (5) | Â | Â |
Progenesis LC-MS (Number of selected features = 467, sensitivity = 8/13, FP = 459) | ||||
Feature No. | Peptide | m/z (charge) | q-value (rank) | FC (rank) |
1 | RGDSPASSKP | 501.25 (2) | 0.0308 (180) | 73.0 (178) |
2 | DRVYIHP | 450.23 (2) | 0.0103 (1) | 33.1 (240) |
3a | RPPGFSPFR | 530.78 (2) | 0.0146 (4) | 32.4 (243) |
3b | RPPGFSPFR | 354.19 (3) | 0.0103 (1) | 46.9 (210) |
4 | DRVYIHPF | 523.77 (2) | 0.0146 (4) | 65.8 (184) |
5a | DRVYIHPFHL | 648.84 (2) | Â | Â |
5b | DRVYIHPFHL | 432.89 (3) | 0.0146 (4) | Inf (1) |
6 | DRVYIHPFHLLVYS | 586.98 (3) | Â | Â |
7a | WLTGPQLADLYHSLMK | 624.99 (3) | Â | Â |
7b | WLTGPQLADLYHSL(M)K | 630.35 (3) | 0.0222 (33) | 50.6 (201) |
8 | YPIVSIEDPFAEDDWEAWSHFFK | 943.43 (3) | Â | Â |
9a | GIGAVLKVLTTGLPALISWIKRKRQQ | 712.43 (4) | Â | Â |
9b | GIGAVLKVLTTGLPALISWIKRKRQQ | 570.15 (5) | 0.0441 (365) | Inf (1) |
XCMS (Number of selected features = 66, sensitivity = 7/13, FP = 59) | ||||
Feature No. | Peptide | m/z (charge) | q-value (rank) | FC (rank) |
1 | RGDSPASSKP | 501.25 (2) | 0.0437 (3) | 40.0 (8) |
2 | DRVYIHP | 450.23 (2) | 0.0224 (1) | 25.3 (19) |
3a | RPPGFSPFR | 530.78 (2) | 0.0437 (3) | 52.2 (7) |
3b | RPPGFSPFR | 354.19 (3) | 0.0437 (3) | 38.0 (9) |
4 | DRVYIHPF | 523.77 (2) | 0.0437 (3) | 137.8 (2) |
5a | DRVYIHPFHL | 648.84 (2) | Â | Â |
5b | DRVYIHPFHL | 432.89 (3) | 0.0437 (3) | 488.4 (1) |
6 | DRVYIHPFHLLVYS | 586.98 (3) | Â | Â |
7a | WLTGPQLADLYHSLMK | 624.99 (3) | Â | Â |
7b | WLTGPQLADLYHSL(M)K | 630.35 (3) | 0.0491 (66) | 17.9 (27) |
8 | YPIVSIEDPFAEDDWEAWSHFFK | 943.43 (3) | Â | Â |
9a | GIGAVLKVLTTGLPALISWIKRKRQQ | 712.43 (4) | Â | Â |
9b | GIGAVLKVLTTGLPALISWIKRKRQQ | 570.15 (5) | Â | Â |