Prediction of peptides observable by mass spectrometry applied at the experimental set level

BMC Bioinformatics

Table 5 Number of tryptic peptides predicted to be observable for selected proteins from the two data sets.

Protein GI Number	Num tryptic peptides (>= 6 aa)	Num tryptic peptides observed	Percent amino acid coverage	Number predicted detectable	Percent predicted detectable	Percent amino acid coverage of detectable
Avian bursa data set
5902793	20	2	10	9	45	33
119359	50	5	9	15	30	21
128413	16	2	11	3	18	14
2119012	7	2	28	3	43	17
17025728	16	2	6	7	44	20
122000	6	4	33	0	0	0
1762374	7	1	23	2	29	21
1172808	13	1	6	4	30	19
7512219	44	1	2	11	25	34
104697	9	2	22	4	44	30
118106991	12	0	0	0	0	0
Hodgkin's lymphoma model data set
479367	34	1	3	5	15	11
729629	18	2	14	11	61	43
899264	13	1	10	4	31	21
63544	48	2	2	6	13	15
50750413	38	3	11	8	21	25
45433516	26	0	0	0	0	0
46048702	14	0	0	0	0	0
125745137	9	0	0	0	0	0
125745114	9	0	0	0	0	0
45433516	26	0	0	0	0	0

1) For the avian bursa dataset, 10 randomly selected observed proteins and the DR3 protein that was expected but not observed. 2) For the Hodgkin's lymphoma model dataset, 5 proteins that were observed in the pathway under consideration and 5 that had been observed using other methods in previous experiments but not observed in this dataset.

ISSN: 1471-2105