Table 1. Proteotyping results of the twelve representative strains included in the study.

For each species, the Type strain, as well as two additional well-characterized reference strains, were included. The numbers of identified proteins, peptides and species-unique peptides after analyses with TCUP are shown (averages of triplicate analyses). The accuracies (%), i.e. proportion of correctly assigned peptides of the total number of species-unique peptides, are also shown. For a confirmed identification, a minimum threshold of five peptide matches per species was used.

Organism	Strain	Distinct proteins	Peptide matches	Species-unique peptide matches	Accuracy (%)
S. pneumoniae	CCUG 28588T	590	3188	227	97
	CCUG 7206	590	2251	175	100
	CCUG 35180	600	2384	214	100
S. mitis	CCUG 31611T	610	3418	272	100
	CCUG 63687	660	2542	287	100
	CCUG 69183	479	3478	506*	99
S. pseudopneumoniae	CCUG 49455T	611	2743	433	100
	CCUG 62647	574	2450	257	97
	CCUG 63747	524	2082	245	100
S. pyogenes	CCUG 4207T	401	1290	314	100
	CCUG 25570	450	1801	351	100
	CCUG 47803	493	2002	418	100

* The genome sequence of CCUG 69183 (= SK271) was present in the “Curated Database”, which is reflected by the higher number of species-unique peptide matches.

^T signifies type strain of the species.