DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs

BMC Bioinformatics

Table 2 Results of parameter optimization for DISMS2 with partial R-squared (adonis)

Rank	topn	bin	ret	dist	cdis	partial R-squared
1	∞	0.20	3000	d _cos	0.3	0.923
2	50	0.20	3000	d _cos	0.3	0.923
3	20	0.20	3000	d _cos	0.3	0.923
4	∞	0.20	3000	d _cos	0.1	0.892
5	50	0.20	3000	d _cos	0.1	0.892
6	20	0.01	3000	d _cos	0.3	0.890
7	20	0.20	3000	d _cos	0.1	0.890
8	50	0.01	3000	d _cos	0.3	0.890
9	∞	0.01	3000	d _cos	0.3	0.890
10	20	0.01	3000	d _PH	0.3	0.879
11	∞	0.20	1000	d _cos	0.3	0.878
⋮	⋮	⋮	⋮	⋮	⋮	⋮
23	20	0.20	3000	d _angle	0.6	0.808
⋮	⋮	⋮	⋮	⋮	⋮	⋮
81	∞	0.20	3000	d _angle	0.3	0.308

Accepted precursor mass shift constant (prec = 10 ppm)
Bold printed lines correspond to the optimized parameters for the different distance measures

ISSN: 1471-2105