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Table 1 Scoring of theoretical mass spectrum under different conditions

From: Tandem mass spectrometry data quality assessment by self-convolution

Protein Sequence: MTDQEAIQDLWQWR
S/No Descriptions Mid-point m/z Mid-point peak value Average of 20 peaks Quality Score
Test Section A
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
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
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
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
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
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 - - -
  1. 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.