Supplementary material for bioinformatics paper: Peak Selection from MALDI-TOF Mass Spectra Using Ant Colony Optimization

1. MATLAB Scripts

The MATLAB scripts perform mass spectral preprocessing (baseline correction, normalization, peak detection, peak calibration, and peak screening) and peak selection using the ACO-SVM algorithm. The scripts and the binned spectra can be downloaded here: MATLAB Scripts

2. Supplementary Data

Table Is. m/z windows sorted by SNR

Index	m/z window		SNR
1	1864.0	1870.2	0.83
2	1777.0	1784.8	0.75
3	2377.6	2382.6	0.72
4	1689.7	1695.9	0.69
5	1349.2	1356.0	0.64
6	2303.7	2309.9	0.62
7	1313.3	1317.1	0.61
8	6593.3	6690.9	0.61
9	1210.5	1214.5	0.58
10	2537.6	2542.1	0.56
11	1124.8	1128.9	0.55
12	1461.5	1469.7	0.54
13	1081.7	1082.4	0.54
14	4049.4	4059.2	0.53
15	1559.3	1566.3	0.50
16	953.4	954.6	0.49
17	2332.9	2337.3	0.49
18	932.2	932.9	0.49
19	8796.4	8823.7	0.48
20	1331.5	1333.1	0.48
21	2550.3	2556.4	0.48
22	933.2	947.1	0.47
23	1319.5	1322.4	0.43
24	947.4	952.8	0.43
25	1448.5	1452.4	0.43
26	2566.1	2570.5	0.42
27	1058.0	1059.1	0.42
28	1876.3	1884.2	0.42
29	1482.1	1483.8	0.42
30	931.3	931.9	0.41
31	1049.1	1050.8	0.40
32	3345.1	3353.1	0.40
33	6419.0	6444.7	0.40
34	1793.1	1797.0	0.40
35	1270.9	1272.8	0.39
36	1334.3	1337.9	0.39
37	1801.1	1805.1	0.39
38	1051.1	1056.2	0.38
39	1484.3	1487.7	0.38
40	3907.0	3911.3	0.38
41	1204.7	1209.5	0.38
42	2753.6	2759.9	0.38
43	3759.1	3763.6	0.38
44	2152.7	2155.9	0.37
45	1669.3	1672.8	0.37
46	3764.8	3767.8	0.37
47	9336.6	9443.6	0.36
48	1057.0	1057.6	0.36
49	2128.9	2131.5	0.36
50	7533.4	7651.9	0.36
51	1151.1	1153.9	0.35
52	4642.1	4647.7	0.34
53	4038.9	4043.8	0.33
54	1016.8	1018.0	0.33
55	1498.1	1502.8	0.33
56	1080.6	1081.4	0.33
57	930.2	931.1	0.32
58	3042.5	3048.0	0.32
59	2530.7	2536.5	0.32
60	2189.4	2192.2	0.32
61	2843.7	2849.1	0.32
62	981.0	982.1	0.31
63	2465.3	2468.2	0.31
64	1387.0	1391.0	0.31
65	1586.7	1588.9	0.31
66	2644.6	2647.7	0.31
67	1471.4	1473.8	0.30
68	1146.8	1150.8	0.30
69	1933.7	1937.9	0.29
70	5040.8	5048.9	0.29
71	2600.0	2607.8	0.29
72	4436.5	4443.6	0.29
73	2297.9	2300.7	0.29
74	1297.8	1299.3	0.29
75	2285.3	2291.0	0.29
76	9105.1	9176.4	0.28
77	6447.9	6451.8	0.28
78	2352.8	2362.5	0.28
79	5059.0	5067.1	0.28
80	4219.8	4234.6	0.28
81	919.9	924.7	0.28
82	1097.1	1098.4	0.28
83	3025.9	3031.9	0.27
84	3032.8	3035.9	0.27
85	2867.9	2872.3	0.26
86	1977.3	1981.4	0.26
87	2010.8	2032.8	0.26
88	2095.5	2099.1	0.26
89	3308.2	3321.4	0.26
90	7751.2	7770.6	0.26
91	1748.1	1750.2	0.25
92	1831.7	1835.5	0.25
93	4186.1	4204.6	0.25
94	3709.1	3716.1	0.25
95	3912.5	3918.0	0.25
96	3388.5	3391.6	0.24
97	4128.4	4134.1	0.24
98	3440.7	3448.0	0.24
99	1772.2	1774.3	0.23
100	4109.8	4116.4	0.23
101	1706.0	1708.0	0.23
102	3189.3	3196.9	0.23
103	3521.9	3526.8	0.23
104	1846.2	1853.2	0.23
105	4445.0	4457.0	0.23
106	2929.7	2937.0	0.23
107	2228.2	2232.7	0.22
108	5000.7	5011.2	0.22
109	2450.5	2453.2	0.22
110	1605.3	1609.3	0.21
111	1888.6	1894.6	0.21
112	1430.8	1433.7	0.21
113	3997.5	4000.7	0.21
114	8846.7	8877.7	0.21
115	2408.7	2412.4	0.21
116	4784.5	4790.2	0.21
117	1919.2	1922.7	0.21
118	925.0	926.0	0.21
119	1474.2	1479.2	0.20
120	3156.9	3163.2	0.20
121	2544.4	2548.2	0.19
122	1763.9	1767.1	0.19
123	2106.9	2111.7	0.19
124	1515.0	1532.5	0.19
125	1504.2	1508.5	0.18
126	4205.9	4218.5	0.18
127	1181.2	1184.5	0.18
128	1045.8	1047.8	0.18
129	1059.4	1077.7	0.18
130	1855.1	1859.0	0.18
131	4007.6	4012.4	0.18
132	4135.4	4144.5	0.18
133	2044.4	2046.9	0.17
134	1165.6	1167.8	0.17
135	3786.7	3791.2	0.17
136	2112.6	2115.8	0.17
137	1373.0	1378.4	0.17
138	4246.0	4256.2	0.17
139	2489.8	2492.8	0.17
140	1895.9	1904.3	0.16
141	8881.2	8961.5	0.16
142	1188.6	1189.5	0.16
143	1696.4	1697.8	0.16
144	3473.9	3478.8	0.16
145	1637.1	1641.7	0.16
146	929.1	929.9	0.16
147	1986.4	1989.0	0.16
148	1623.1	1629.6	0.16
149	9278.9	9304.9	0.15
150	982.4	983.0	0.15
151	4238.4	4243.9	0.15
152	3768.9	3777.2	0.15
153	3929.4	3975.2	0.14
154	2633.2	2635.8	0.14
155	5077.2	5084.9	0.13
156	1953.3	1955.6	0.13
157	2883.5	2891.9	0.13
158	4313.6	4318.4	0.13
159	2722.6	2729.2	0.12
160	3283.4	3297.3	0.12
161	1029.7	1031.0	0.12
162	1808.0	1813.1	0.12
163	1396.7	1398.1	0.12
164	1611.0	1620.0	0.12
165	1437.4	1439.1	0.11
166	983.3	983.9	0.11
167	1192.6	1198.9	0.11
168	2103.7	2106.3	0.11
169	1594.1	1598.0	0.11
170	4464.6	4469.9	0.10
171	2766.8	2772.9	0.10
172	1824.2	1826.4	0.10
173	1456.5	1457.4	0.10
174	3361.5	3366.6	0.10
175	8551.0	8622.2	0.10
176	2051.8	2055.9	0.09
177	3303.2	3307.2	0.09
178	1308.7	1312.0	0.09
179	3322.7	3325.7	0.08
180	1199.4	1200.5	0.08
181	1174.5	1175.2	0.08
182	3166.7	3173.7	0.08
183	2181.7	2188.7	0.08
184	1018.3	1022.1	0.08
185	3982.8	3995.9	0.07
186	964.8	966.0	0.07
187	2610.1	2621.9	0.07
188	1110.6	1112.8	0.07
189	4471.3	4474.0	0.07
190	5897.7	5912.5	0.07
191	2581.1	2587.5	0.07
192	1392.8	1396.3	0.06
193	1291.5	1296.2	0.06
194	1434.1	1436.8	0.06
195	4960.8	4970.2	0.06
196	2942.9	2946.7	0.06
197	1031.3	1035.8	0.06
198	2166.9	2172.4	0.06
199	996.0	998.9	0.06
200	1785.4	1790.9	0.06
201	4274.5	4277.1	0.06
202	5327.9	5341.8	0.06
203	3261.8	3269.7	0.05
204	1459.1	1460.9	0.05
205	1732.1	1742.7	0.05
206	1219.6	1227.3	0.05
207	1407.2	1411.2	0.05
208	1303.6	1308.3	0.05
209	2787.9	2793.8	0.04
210	4257.9	4273.3	0.04
211	1545.2	1549.8	0.04
212	2741.8	2745.1	0.04
213	1750.7	1755.6	0.04
214	2923.5	2927.1	0.04
215	3270.7	3282.5	0.04
216	3141.8	3149.7	0.03
217	1186.8	1188.2	0.03
218	926.3	928.8	0.03
219	2904.6	2908.7	0.02
220	1416.7	1423.8	0.02
221	4280.5	4312.3	0.01
222	2684.8	2688.0	0.01
223	3427.4	3434.2	0.01
224	1277.0	1282.5	0.01
225	1235.3	1242.9	0.01
226	2266.9	2277.6	0.01
227	3326.7	3332.7	0.01
228	2423.7	2426.4	0.00

Table IIs. m/z windows sorted by frequency of occurrence for 100 ACO-SVM runs with n = 5 and N = 50.

m/z window		Index	Frequency (%)
1864.0	1870.2	1	86
2377.6	2382.6	3	51
1482.1	1483.8	29	47
2303.7	2309.9	6	41
1777.0	1784.8	2	40
2537.6	2542.1	10	38
1793.1	1797.0	34	32
1559.3	1566.3	15	31
932.2	932.9	18	20
6593.3	6690.9	8	17
2566.1	2570.5	26	12
4007.6	4012.4	131	12
1313.3	1317.1	7	11
1081.7	1082.4	13	11
1689.7	1695.9	4	10
1484.3	1487.7	39	10
1461.5	1469.7	12	5
2550.3	2556.4	21	5
3907.0	3911.3	40	5
1349.2	1356.0	5	4
933.2	947.1	22	3
1801.1	1805.1	37	3
3345.1	3353.1	32	2
1124.8	1128.9	11	1
2332.9	2337.3	17	1
1448.5	1452.4	25	1
4219.8	4234.6	80	1

Table IIIs. m/z windows sorted by frequency of occurrence when ACO-SVM is used with n = 3, 5, 7, and 9; N = 25, 50, and 100. Each combination was run 25 times (i.e., a total of 300 ACO-SVM runs).

m/z window		Index	Frequency (%)
1864.0	1870.2	1	89.3
1777.0	1784.8	2	62.0
2377.6	2382.6	3	53.7
1482.1	1483.8	29	53.3
2303.7	2309.9	6	42.7
1559.3	1566.3	15	27.7
6593.3	6690.9	8	27.3
1689.7	1695.9	4	26.7
2537.6	2542.1	10	24.0
932.2	932.9	18	20.7
1793.1	1797.0	34	19.7
1313.3	1317.1	7	16.0
2566.1	2570.5	26	15.3
3907.0	3911.3	40	11.7
1081.7	1082.4	13	9.7
2332.9	2337.3	17	9.3
1484.3	1487.7	39	9.3
1349.2	1356.0	5	9.0
4049.4	4059.2	14	6.0
953.4	954.6	16	5.7
933.2	947.1	22	5.3
2550.3	2556.4	21	5.0
4007.6	4012.4	131	5.0
1124.8	1128.9	11	4.7
8796.4	8823.7	19	3.7
1448.5	1452.4	25	3.7
1461.5	1469.7	12	3.3
1319.5	1322.4	23	2.7
1210.5	1214.5	9	2.0
1331.5	1333.1	20	2.0
947.4	952.8	24	2.0
4219.8	4234.6	80	2.0