GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA)

Tsugawa, Hiroshi; Tsujimoto, Yuki; Arita, Masanori; Bamba, Takeshi; Fukusaki, Eiichiro

doi:10.1186/1471-2105-12-131

Table 2 43 out of 99 compounds included in the five classes

From: GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA)

Class	Name	IUPAC	Predicted Name
Organic acid	Citramalic acid	2-hydroxy-2-methylbutanedioic acid	Organic acid
	Citric acid	2-hydroxypropane-1,2,3-tricarboxylic acid	Organic acid
	Fumaric acid	(E)-but-2-enedioic acid	Organic acid
	Glycolic acid	2-hydroxyacetic acid	Organic acid* and Sugar
	Maleic acid	(Z)-but-2-enedioic acid	Organic acid
	Malic acid	2-hydroxybutanedioic acid	Organic acid
	Malonic acid	propanedioic acid	Organic acid
	Mandelic acid	2-hydroxy-2-phenylacetic acid	Organic acid
	Oxalic acid	oxalic acid	Organic acid
	Oxamic acid	oxamic acid	Organic acid
	Shikimic acid	(3R,4S,5R)-3,4,5-trihydroxycyclohexene-1-carboxylic acid	No annotation
	Succinic acid	butanedioic acid	Organic acid
Sugar	Arabinose	(2S,3R,4R)-2,3,4,5-tetrahydroxypentanal	Sugar
	Arabitol	(2R,4R)-pentane-1,2,3,4,5-pentol	Sugar
	Fructose	(3S,4R,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol	Sugar
	Galactose	(3R,4S,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol	Sugar
	Glucose	(3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol	Sugar
	Inositol	cyclohexane-1,2,3,4,5,6-hexol	Sugar* and Organic acid
	Maltose	(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[(2R,3S,4R,5R)-4,5,6-trihydrox y-2-(hydroxymethyl)oxan-3-yl]oxyoxane-3,4,5-triol	Sugar
	Mannose	(3S,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol (2R,3R,4S,5S,6R)-2-[(2S,3S,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)	Sugar
	Melezitose	-2-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]ox yoxolan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol	Sugar
	Ribitol	pentane-1,2,3,4,5-pentol	Sugar
	Ribose	(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol	Sugar
	Sucrose	(2R,3R,4S,5S,6R)-2-[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymet hyl)oxolan-2-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol	Sugar
	Threitol	(2R,3R)-butane-1,2,3,4-tetrol	Sugar
	Trehalose	(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[(2R,3R,4S,5S,6R)-3,4,5-trihyd roxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-3,4,5-triol	Sugar
	Xylose	(2S,3R,4S,5R)-oxane-2,3,4,5-tetrol	Sugar
	Glycerol	propane-1,2,3-triol	Sugar
Sugar phosphate	Ribulose-5-phosphate	[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl] dihydrogen phosphate	Sugar phosphate
Amine	Cadaverine	pentane-1,5-diamine	Amine
	Dopamine	4-(2-aminoethyl)benzene-1,2-diol	Amine
	Isobutylamine	2-methylpropan-1-amine	Amine
	n-Butylamine	butan-1-amine	Amine
	n-Propylamine	propan-1-amine	Amine
	Putrescine	butane-1,4-diamine	Amine
	Spermidine	N'-(3-aminopropyl)butane-1,4-diamine	No annotation
	Spermine	N,N'-bis(3-aminopropyl)butane-1,4-diamine	No annotation
	Tyramine	4-(2-aminoethyl)phenol	Amine
	Histamine	2-(1H-imidazol-5-yl)ethanamine	Amine
	Serotonin	3-(2-aminoethyl)-1H-indol-5-ol	Amine
	Tryptamine	2-(1H-indol-3-yl)ethanamine	Amine
Fatty acid	Heptadecanoic acid	heptadecanoic acid	Fatty acid
	Octadecanoic acid	octadecanoic acid	Fatty acid

Table 2 shows 43 standard compounds classified to the five metabolite groups constituting the SIMCA method. Table 3 shows the remaining 56 standard compounds. Table 2 and 3 also show the predicted name of each compound by the SIMCA algorithm. If a compound was classified into some groups, the groups were fastened by "and". The asterisk (*) indicates the group with higher p-value. If a compound was not classified into any groups, the predicted name was described as "No annotation".

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ISSN: 1471-2105

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