Table 3.

Results of the BLAST search on the false positive set of E. coli and S. aureus, and specifically on the false positives in disagreement with the annotation of the Mass Spectrometry (MS) and Edman sequencing (Ecogene) dataset

Set-up	type	#	aligned  total	TIS	TIS + stop	description  hypothetical
S. aureus	Proteoform	79	79	77	73	12
	Novel protein	25	19	17	15	6
E. coli	Proteoforms	232	232	217	198	39
	Novel protein	258	204	157	137	106
MS	Proteoforms	34	34	22	28	1
Ecogene	Proteoforms	43	43	40	36	1

These predictions can be divided into proteoforms, which have a TIS that is either up- or downstream of the annotated ORF, or novel proteins, constituting ORFs with a non-annotated stop site. A BLAST search of these proteins was performed on the non-redundant protein database. A maximum cut-off value of 0.1 for the E score is taken. The total amount of false positives are given for each type. Taking only the best aligned protein (i.e. highest E score) for each of the false positive results, the total amount of matches that were aligned by start site or both start and stop site are given. Finally, the total amount of proteins described as ‘hypothetical’ are given.