Table A2.

Percentage bias of the imputation methods across different parameters on different metabolites including MICE-pmm with a single imputation.

Missing Mechanism	Sample Size	Missing Percentage	Metabolites/Imputation Method
			PC(32:2)			Succinylcarnitine			Glutamate			Urate
			MICE-pmm	kNN-obs-sel	MICE-pmm [m = 1]	MICE-pmm	kNN-obs-sel	MICE-pmm [m = 1]	MICE-pmm	kNN-obs-sel	MICE-pmm [m = 1]	MICE-pmm	kNN-obs-sel	MICE-pmm [m = 1]
MCAR	n = 50	15%	2.0	2.1	1.4	0.3	6.0	0.4	2.2	0.2	2.3	4.9	4.9	5.5
		30%	3.2	4.5	3.4	2.8	14.4	2.6	8.6	1.1	8.8	11.3	10.2	10.1
		60%	13.9	14.5	13.2	28.9	31.3	29.7	40.2	2.0	40.7	39.9	27.6	40.9
	n = 150	15%	0.7	0.5	0.9	1.4	13.8	1.7	0.2	1.9	0.3	0.7	0.5	0.5
		30%	1.9	1.8	2.2	0.4	31.9	0.9	1.1	5.1	1.1	0.7	1.3	0.1
		60%	3.9	3.2	3.4	5.2	72.7	0.6	6.2	15.0	6.0	2.09	12.5	2.1
	n = 599	15%	0.3	0.8	0.3	0.1	9.3	0.2	0.2	2.6	0.3	0.6	2.2	0.4
		30%	0.7	2.4	0.8	0.6	20.1	0.3	0.1	5.6	0.1	1.5	4.9	1.8
		60%	1.9	7.9	1.7	3.5	50.9	4.6	0.7	15.1	0.8	2.6	15.0	2.4
PLoD	n = 50	15%	1.3	0.8	1.0	2.8	1.8	3.4	0.7	1.8	0.8	12.7	6.2	12.5
		30%	3.5	2.2	2.8	7.7	4.3	7.5	4.2	3.6	4.1	26.3	16.5	25.5
		60%	19.5	3.0	18.6	34.8	8.3	34.8	19.3	15.0	19.6	87.4	66.1	89.4
	n = 150	15%	0.2	1.6	0.2	0.7	12.8	0.7	1.3	0.8	1.4	5.3	6.3	5.4
		30%	0.3	3.3	0.6	0.2	23.4	0.4	3.0	2.3	3.1	8.0	14.9	8.7
		60%	4.2	2.6	4.2	16.2	46.1	17.2	9.4	8.6	9.1	39.8	59.7	38.2
	n = 599	15%	0.5	0.1	0.5	0.9	7.3	1.0	0.9	1.4	0.9	0.5	1.9	0.5
		30%	1.1	1.6	1.2	2.5	16.7	2.9	2.1	2.9	2.2	0.6	3.3	0.6
		60%	4.9	11.5	4.9	9.7	54.3	9.2	4.1	13.1	4.4	0.1	4.3	0.6

Abbreviations: MCAR: missing completely at random; PLoD: probabilistic limit of detection; MICE-pmm [m = 1]: MICE-pmm with a single imputation.