Table 2.

Overview of peak annotation in PAVE.

Organism		S. cerevisiae		E. coli
Ionization mode		Positive	Negative	Positive	Negative
Total peak number		30,212	14,927	28,761	14,921
ATOMCOUNT	Peaks in procedure blank	21,186	10,015	20,600	10,147
	Other peaks without labeling	3,591	2,393	6,312	3,422
	Labeling but ρ < 0.75	820	380	339	201
	Logical labeling (i.e. biological)	4,615	2,139	1,510	1,151
JUNKREMOVER	Isotopes	1,598	632	467	404
	Dimer or double charge	313	21	25	45
	Adducts (assigned using same polarity mode)	1,153	539	431	278
	Adducts (assigned only using opposite polarity mode)	138	76	55	11
	Too low C/N count for mass	363	70	32	12
	Ringing peaks	28	47	7	11
In-source CID	Fragments	96	64	90	71
	Parent ions	926	690	403	319
Formula assignment	Formula match to metabolite	278	359	132	164
	No formula match in database	648	331	271	155
Metabolite structure identification (With formula)	RT match	144		92
	MS/MS match	35		30
	Unknown structure	359		133