Table 1. Number of quantified peptides on samples with predefined ratios with (+) or without (−) boundary detection (BD) and model fitness check (MFC).

	MaxQuant	BD (−) MFC (−)	BD (+) MFC (−)	BD (+) MFC (+)
1:1 Sample	2228	1923	1791	750
2.5:1 Sample	1827	1540	1441	903
5:1 Sample	2076	158	1456	1067