Biomedical Engineering Reference
In-Depth Information
Tabl e 1. 2
Real-world peptide sequencing problems
Input data
Outcomes
Times
w
0
f
t
max
e
max
nx
v
r
w/o WD
w WD
S
572.20
7
2
1
20
14
108
1
1
0:1
0:1
572.20
7
6
2
20
84
3;571
2
2
1:9
1:6
851.30
18
2
1
20
36
543
1
4
0:5
0:5
851.30
18
4
2
24
144
6;780
4
7
2:0
1:4
851.30
18
6
3
24
324
12;642
10
16
5:6
3:0
859.12
20
3
1
40
60
2;904
4
26
1:6
1:1
859.12
20
6
2
40
240
8;156
5
29
4:1
3:4
913.30
16
2
1
20
32
539
2
7
1:0
0:8
913.30
16
6
3
20
288
10;741
8
32
6:8
4:0
968.58
19
2
1
20
38
768
6
24
1:3
1:1
968.58
19
6
2
20
228
7;021
10
38
4:1
3:4
1037.10
18
2
1
20
36
714
7
25
1:4
1:0
1037.10
18
6
2
20
216
6;936
12
44
4:3
3:2
1108.60
21
2
1
26
42
2;687
8
18
3:5
2:1
1108.60
21
4
2
26
168
7;456
16
64
12:2
5:6
1234.20
19
2
2
20
76
4;529
9
26
8:3
3:2
1234.20
19
6
2
20
228
8;956
15
106
29:2
14:0
1479.84
20
2
1
20
40
690
7
22
14:3
6:8
1479.84
20
6
2
20
240
8;796
18
102
33:9
13:7
1570.60
22
2
1
21
44
2;498
9
35
28:5
16:3
1570.60
22
6
2
21
264
9;657
14
98
56:8
39:2
1607.69
27
2
2
26
108
5;744
6
20
44:3
20:9
1607.69
27
6
3
26
486
22;565
11
63
473:0
192:8
Tab le
1.2
reports various experiments of real peptide sequencing problems on a
Pentium IV 1.7GHz PC. In particular, we indicate: the weight of the peptide (
w
0
);
the number of peaks extracted from the spectrum (f ); the number of considered
types (t
max
) and charges (e
max
) of fragments; the number of possible components
(n); the number of variables (x) and clauses (
v
) of the obtained formula; the number
of models (r ) of the obtained formula, the overall number of solutions (
S
), and
computational times (in seconds) for the whole sequencing procedure without the
weights database (w/o WD) and with it (w WD). Time for computing off-line the
weights database with
D
300 is 40 seconds and with
D
400 is 126 seconds.
Both values were sufficient for sequencing the gaps in the reported analyses. A time
of this order (the exact one depends on our a priori choice for ) should therefore
be considered just once for a whole series of tests with WD. It can also be stored
on hard disk and read by the input routine in a subsequent time. Those results are
intended to give real-world examples of application, rather than exploring all the
computational possibilities of the described procedure.
As observable from the table, results depend of course on the choice of possible
types and charges of fragments: for the same spectrum, different choices produce
different results, and the number of sequences compatible with the given input data
is sometimes large. This is an intrinsical character of the problem. However, all the
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