Table 3.

The table shows the number of TPs, TNs, FPs and FNs calculated starting from a matrix composed of proteins quantified by a minimum of 2 peptides.

	Condition	Human	Pisum sativum	Soybean	TP	TN	FP	FN
Spectronaut Direct-DIA	PAC-1 µg	2533	81	103	149	2264	269	35
	PAC+SCX-1 µg	2741	98	112	147	2600	141	63
	FASP-1 µg	2172	71	86	146	1661	511	11
	PAC-10 µg	2587	88	109	163	2571	16	34
	PAC+SCX-10 µg	2773	98	122	189	2744	29	31
	FASP-10 µg	2410	81	93	151	2248	162	23
Spectronaut	PAC-1 µg	2250	62	82	112	2135	115	32
	PAC+SCX-1 µg	2257	62	81	103	2148	109	40
	FASP-1 µg	2107	59	73	106	1746	361	26
	PAC-10 µg	2213	59	80	118	2184	29	21
	PAC+SCX-10 µg	2252	63	79	123	2224	28	19
	FASP-10 µg	2229	59	81	121	2139	90	19
MaxDIA	PAC-1 µg	2990	82	130	144	2925	65	68
	PAC+SCX-1 µg	3055	82	126	135	3024	31	73
	FASP-1 µg	2888	80	121	143	2544	344	58
	PAC-10 µg	2947	78	118	131	2940	7	65
	PAC+SCX-10 µg	2973	80	130	148	2957	16	62
	FASP-10 µg	3001	80	128	147	2983	18	61