Table 1

Parameters	Values
	PeptideAtlas	OPD	ISB
No. of protein sequences	31	4,279	3,553
Total database size	9,421	494,049	1,248,212
Query size	44	202	995
Fragments mass tolerance	0.5 Da
Parent mass tolerance	1.0 Da
Modifications	–
Charge	+2, +3
Ion type	a, b, y,
Neutral loss	–H₂O, –NH₃
Missing cleavage	0
Protease	Trypsin
Mass range	0-5000 Da

Table 1: Parameters for the generation of databases and theoretical spectra.