A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations

Table 2 Summary of the number of proteins detected with at least 10 or 6 PSMs in the SIHUMIx proteogenomic dataset, using the 6frame translation of the genomes

Species	Nov	Hyp	Known	%
At least 10 PSMs per candidate
B. theta.	37	1975	248	45.9
B. producta	52	1138	132	23.2
E. coli	26	150	988	26.8
E. ramosum	10	355	53	13.7
B. longum	16	128	0	7.4
A. caccae	17	549	100	19.3
L. plantarum	31	83	28	3.7
C. butyricum	14	135	32	4.1

Species	Nov	Hyp	Known	%
A least 6 PSMs per candidate
B. theta.	72	2118	256	49.0
B. producta	103	1289	143	26.1
E. coli	65	182	1127	30.9
E. ramosum	30	431	65	16.7
B. longum	42	170	0	9.8
A. caccae	39	632	119	22.3
L. plantarum	48	116	36	5.1
C. butyricum	26	176	39	5.3

Novel (nov) proteins are not contained within annotation, hypothetical (hyp) proteins are annotated but tagged with low confidence (see “Methods” section for details), known refer to all proteins for which higher levels of confidence are associated with the available annotation. The eight species are ordered by decreasing abundance. The last column gives the fraction of the annotated proteins that were detected

ISSN: 1471-2105