Table 1.

Comparison of AMDIS and MetabolomeExpress MSRI library matching performance: summary of results.

	AMDIS		MetabolomeExpress
Settings:	Low Sensitivity	High Sensitivity	Low Sensitivity	High Sensitivity
Total Peak Identifications Reported	152	165	153	170
True Positive	140	150	149	163
False Positive	7	12	0	1
False Negative	35	24	20	7
Ambiguous	5	5	6	7

A raw data file from a representative GC/MS analysis of a complex methanolic plant tissue extract was processed and searched against a single MSRI reference library using either AMDIS or MetabolomeExpress. Each software package was used under two different sensitivity settings to allow a more meaningful comparison of results. All peak identification results were manually verified by inspection of relevant raw GC/MS signals as true positives, false positives, false negatives or ambiguous calls. False negatives were cases where a search failed to identify a component that was successfully identified by another search. Detailed results including manual validation comments are presented in additional file 4.