Table 2. SHIP metabomatching results.

Metabomatching ranks of reference metabolites obtained for SHIP pseudospectra, with UMDB as the spectral reference database, and with: peak- (P) or multiplet-mode (M), χ²- (X) or Z-scoring (Z), and without (C) or with decorrelation (D). Neighborhood parameter is δ = 0.03 in peak-mode and 0.01 in multiplet-mode. Shrinkage parameter is λ = 0.5 for decorrelation, 1 without. Ranks obtained with 2-compound metabomatching are shown in bold, those obtained with ±-2-compound metabomatching in bold and italic. Squares (□) indicate ranks not in the top 10% of UMDB listed metabolites, that is ranks greater than 18. Individual metabomatching figures including the eight highest ranked metabolite candidates for each pseudospectrum can be found in S2 Fig.

Locus			Reference Association		Feature Association		Ranks
Gene	Chr	SNP	Metabolite	p	Feature	p	${\text{P}}_{\text{C}}^{\text{X}}$	${\text{P}}_{\text{D}}^{\text{X}}$	${\text{P}}_{\text{C}}^{\text{Z}}$	${\text{P}}_{\text{D}}^{\text{Z}}$	${\text{M}}_{\text{C}}^{\text{X}}$	${\text{M}}_{\text{D}}^{\text{X}}$	${\text{M}}_{\text{C}}^{\text{Z}}$	${\text{M}}_{\text{D}}^{\text{Z}}$
DAB1	1	rs558475	hippurate	3.9 × 10−7	3.949	3.6 × 10−8	1	1	1	1	1	1	1	1
CPS1	2	rs2216405	glycine	2.9 × 10−11	3.555	4.9 × 10−9	1	1	□	□	3	1	□	□
			creatine	7.5 × 10−11			1	1	□	□	16	11	□	□
XYLB	3	rs2070486	glycolate	1.4 × 10−9	3.937	2.4 × 10−9	2	1	5	2	16	16	□	□
SLC6A20	3	rs17279437	dimethylglycine	1.1 × 10−46	2.916	1.1 × 10−21	1	2	2	2	1	1	1	1
ENTPPL	4	rs7654111	ethanolamine	2.3 × 10−26	3.126	5.0 × 10−16	1	1	4	5	1	1	2	2
SLC6A19	5	rs7719875	histidine	2.4 × 10−14	6.877	6.4 × 10−12	8	8	10	11	10	8	8	8
			tyrosine	6.5 × 10−10			9	13	12	12	12	14	□	14
AGXT2	5	rs37369	3-aminoisobutyrate	2.4 × 10−252	1.171	3.7 × 10−252	1	1	2	2	1	1	1	1
DMGDH	5	rs248386	dimethylglycine	1.0 × 10−13	2.916	1.8 × 10−8	5	5	□	□	2	1	□	□
SLC36A2	5	rs3846710	glycine	1.1 × 10−10	3.555	6.3 × 10−9	1	1	2	2	1	1	2	5
NAT2	8	rs1495743	formate	9.5 × 10−60	3.189	1.6 × 10−104	1	1	1	1	1	1	1	1
SLC6A13	12	rs11613331	3-aminoisobutyrate	2.5 × 10−15	1.190	5.0 × 10−16	5	5	3	3	4	4	3	3
HPD	12	rs4760099	α-hydroxyisobutyrate	2.2 × 10−80	1.345	2.2 × 10−64	1	1	1	1	2	1	1	1
			3-hydroxyisovalerate	2.4 × 10−7			1	1	1	1	3	4	2	5
PNMT	17	rs8069451	tyrosine	7.9 × 10−22	6.877	4.4 × 10−17	□	□	□	□	□	□	□	□
			histidine	7.3 × 10−21			□	□	□	□	□	□	□	□
			alanine	2.3 × 10−11			18	18	16	□	17	□	15	□
SCL7A9	19	rs8112297	lysine	5.0 × 10−16	3.003	9.4 × 10−7	9	9	15	17	15	11	17	□