Table 1. Comparison of Strategies for Grouping Similar Proteins^a.

grouping strategy	percent of peptides shared	total number of groups	number of groups with >10 counts	percent of groups containing any shared peptides	percent of groups containing only one protein	number of groups differentially expressed (p < 0.05/q < 0.05)
No grouping	31.16%	4593b	2583	52.03%	100.00%	116/16
Baseline grouping (1/1)	11.94%	3264	2405	33.76%	77.51%	120/17
Light grouping (1/5)	6.84%	2998	2329	26.66%	70.92%	119/17
Swiss-Prot search with no grouping	4.78%	2976	2201	27.21%	100.00%	110/16
Moderate grouping (2/10)	4.62%	2885	2259	22.13%	69.06%	123/16
Ensembl family grouping	0.59%	2343	1808	4.54%	55.65%	101/19
Aggressive grouping	0.00%	2579	1958	0.00%	63.31%	111/14

^aGrouping label (2/10) indicates that two proteins with any shared peptides are merged unless they each have 2 exclusive peptides with a total of 10 exclusive peptide counts to distinguish between them.

^bThe “no grouping” protein set includes redundant proteins.