TABLE 2.

Comparison of the distribution of proteins assigned at phylum and class levels for each methodology.

	Gel-based				Gel-free
	TAX-DB	NAM-DB	AM-DB	Comb-DB	TAX-DB	NAM-DB	AM-DB	Comb-DB
Phylum
Proteobacteria	87.2	92.7	95.2	89.8	87.6	92.9	91.5	90.0
Cyanobacteria	6.3	2.9	2.0	4.0	2.6	4.8	1.6	2.0
Bacteroidetes	4.9	4.2	2.4	5.0	7.6	1.4	6.1	5.8
Other (<1%)	1.6	0.2	0.4	1.2	2.2	0.9	0.8	2.2
Class
Alphaproteobacteria	73.7	81.6	79.9	74.3	69.7	68.4	68.4	67.5
Gammaproteobacteria	12.9	11.5	14.8	14.4	18.0	25.7	24.4	23.5
Flavobacteriia	6.5	3.7	2.2	3.9	6.3	3.5	4.9	4.8
Unclassified Cyanobacteria	3.9	2.7	1.8	5.3	2.5	1.4	1.2	2.1
Other (<1%)	3.0	0.5	1.2	2.1	3.6	1.0	1.0	2.2

Values represent the proportion of proteins with identical taxonomy on total identified protein using TAX-DB, NAM-DB, AM-DB, or Comb-DB in both gel-free and gel-based approaches. The number of peptides detected for each protein was used as quantitative value. Taxa displaying a proportion <1% were gathered into “Other” category.