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

BMC Bioinformatics

Table 4 Mean distances of runs for different ways of proteome comparisons methods between and within species

Method	DB.ra	DB.ra.nodup	DISMS2.f	DB.a DISMS2.af	DB.af
C vs. C	0.125	0.178	0.290	0.379	0.456	0.452
D vs. D	0.121	0.184	0.297	0.477	0.539	0.533
H vs. H	0.143	0.194	0.299	0.435	0.501	0.498
M vs. M	0.131	0.184	0.303	0.444	0.518	0.508
Y vs. Y	0.117	0.173	0.278	0.589	0.633	0.629
C vs. D	0.957	0.978	0.946	0.972	0.967	0.976
C vs. H	0.956	0.978	0.935	0.970	0.955	0.973
C vs. M	0.954	0.977	0.944	0.969	0.961	0.973
C vs. Y	0.986	0.992	0.972	0.992	0.981	0.993
D vs. H	0.945	0.971	0.927	0.966	0.954	0.969
D vs. M	0.941	0.969	0.929	0.963	0.953	0.967
D vs. Y	0.983	0.992	0.962	0.991	0.979	0.992
H vs. M	0.551	0.623	0.624	0.709	0.740	0.744
H vs. Y	0.982	0.991	0.958	0.990	0.979	0.991
M vs. Y	0.982	0.991	0.962	0.990	0.979	0.991

For different ways of proteome comparisons methods steps of search method, spectrum universe, annotation check, filter check and potential removal of duplicates between are combined. Mean distances of runs between (down) and within (top) species of roundworm (C), fruit fly (D), human (H), mouse (M) and yeast (Y) are shown

ISSN: 1471-2105