Table 4: Databases used in database searches.

For the UPS1/yeast database, ISB18 database, and the five iterations of the human database, peptides in common between the relevant and irrelevant database were removed from analysis. Any relevant ricin peptide also found in the non-ricin castor plant proteome was considered to be relevant. The number of irrelevant peptides includes the set of neighbor peptides. The peptide counts above are for the target databases, but by construction these counts are nearly identical in the corresponding decoy databases.

relevant database	peptides	irrelevant database	peptides	# neighbor peptides
UPS1	2,552	yeast	611,861	3,459
ricin	80	non-ricin castor plant	2,340,370	155
ISB18 + H. influenzae	120,379	N. tabacum	4,108,414	768,373
human protein P18206	364	all other human proteins	2,653,948	1,863
human protein Q9Y490	506	all other human proteins	2,653,757	2,418
human protein P07900	102	all other human proteins	2,654,127	358
human protein P08238	90	all other human proteins	2,654,130	182
human protein P10809	136	all other human proteins	2,654,122	521