Table 1 |
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Scoring of theoretical mass spectrum under different conditions |
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Protein Sequence: MTDQEAIQDLWQWR |
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|
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|
S/No |
Descriptions |
Mid-point m/z |
Mid-point peak value |
Average of 20 peaks |
Quality Score |
|
|
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Test Section A |
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1 |
White Gaussian noise level = 0% |
910.92 |
1.00 |
0.2149 |
4.6542 |
|
2 |
White Gaussian noise level = 5% |
910.92 |
1.00 |
0.2195 |
4.5564 |
|
3 |
White Gaussian noise level = 10% |
910.92 |
1.00 |
0.2162 |
4.6255 |
|
4 |
White Gaussian noise level = 15% |
910.92 |
1.00 |
0.2820 |
3.5467 |
|
5 |
White Gaussian noise level = 20% |
910.91 |
1.00 |
0.5616 |
1.7808 |
|
6 |
White Gaussian noise level = 25% |
910.92 |
1.00 |
0.7875 |
1.2699 |
|
7 |
White Gaussian noise level = 30% |
910.92 |
1.00 |
0.8570 |
0.9140 |
|
Test Section B |
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1 |
add 10 random peaks, noise level 1 |
910.92 |
1.00 |
0.2150 |
4.6511 |
|
2 |
add 20 random peaks, noise level 1 |
910.92 |
1.00 |
0.2153 |
4.6442 |
|
Test Section C |
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|
1 |
b-ions peaks reduced by 10%, noise level 1 |
910.92 |
1.00 |
0.2206 |
4.5330 |
|
2 |
b-ions peaks reduced by 20%, noise level 1 |
910.92 |
1.00 |
0.2263 |
4.4192 |
|
3 |
b-ions peaks reduced by 30%, noise level 1 |
910.92 |
1.00 |
0.2360 |
4.2380 |
|
4 |
b-ions peaks reduced by 40%, noise level 1 |
910.92 |
1.00 |
0.2510 |
3.9842 |
|
5 |
b-ions peaks reduced by 50%, noise level 1 |
910.92 |
1.00 |
0.2727 |
3.6673 |
|
6 |
b-ions peaks reduced by 60%, noise level 1 |
910.92 |
1.00 |
0.3335 |
2.9989 |
|
7 |
b-ions peaks reduced by 70%, noise level 1 |
910.92 |
1.00 |
0.4363 |
2.2654 |
|
8 |
b-ions peaks reduced by 80%, noise level 1 |
NA |
- |
- |
- |
|
Test Section D |
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|
1 |
y-ions peaks reduced by 10%, noise level 1 |
910.92 |
1.00 |
0.2169 |
4.6106 |
|
2 |
y-ions peaks reduced by 20%, noise level 1 |
910.92 |
1.00 |
0.2198 |
4.5489 |
|
3 |
y-ions peaks reduced by 30%, noise level 1 |
910.92 |
1.00 |
0.2235 |
4.4740 |
|
4 |
y-ions peaks reduced by 40%, noise level 1 |
910.92 |
1.00 |
0.2303 |
4.3418 |
|
5 |
y-ions peaks reduced by 50%, noise level 1 |
910.92 |
1.00 |
0.2435 |
4.1072 |
|
6 |
y-ions peaks reduced by 60%, noise level 1 |
910.92 |
1.00 |
0.2956 |
3.3824 |
|
7 |
y-ions peaks reduced by 70%, noise level 1 |
910.92 |
1.00 |
0.3926 |
2.5468 |
|
8 |
y-ions peaks reduced by 80%, noise level 1 |
NA |
- |
- |
- |
|
Test Section E |
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|
1 |
minus 2 b-ions peaks, noise level 1 |
910.92 |
1.00 |
0.2097 |
4.7692 |
|
2 |
minus 4 b-ions peaks, noise level 1 |
910.92 |
1.00 |
0.2320 |
4.3103 |
|
3 |
minus 6 b-ions peaks, noise level 1 |
910.92 |
1.00 |
0.3013 |
3.3190 |
|
4 |
minus 8 b-ions peaks, noise level 1 |
910.92 |
1.00 |
0.3435 |
2.9114 |
|
5 |
minus 10 b-ions peaks, noise level 1 |
NA |
- |
- |
- |
|
Test Section F |
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|
1 |
minus 2 y-ions peaks, noise level 1 |
910.92 |
1.00 |
0.2512 |
3.9813 |
|
2 |
minus 4 y-ions peaks, noise level 1 |
910.92 |
1.00 |
0.3027 |
3.3041 |
|
3 |
minus 6 y-ions peaks, noise level 1 |
910.92 |
1.00 |
0.3810 |
2.6245 |
|
4 |
minus 8 y-ions peaks, noise level 1 |
910.92 |
1.00 |
0.4432 |
2.2562 |
|
5 |
minus 10 y-ions peaks, noise level 1 |
NA |
- |
- |
- |
|
|
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In our work, we tested the qualitative measurement of the tandem mass spectra based on different noise intensities (Sec. A), additional spurious peaks (Sec. B), different b-ion intensities (Sec. C), different y-ion intensities (Sec. D), different percentage loss of b-ion (Sec. E), and different percentage loss of y-ion (Sec. F). We observed the drop in score as the quality of the theoretical mass spectrum deteriorates. |
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Choo and Tham BMC Bioinformatics 2007 8:352 doi:10.1186/1471-2105-8-352 |
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